Polygenic Risk Analysis PTSD.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "apparent-breathing",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "cathedral-breathing",
   "metadata": {},
   "outputs": [],
   "source": [
    "ptsd_df= pd.read_csv(\"SORTED_PTSD_EA9_AA7_LA1_SA2_ALL_study_specific_PCs1.txt\", sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "possible-administrator",
   "metadata": {},
   "outputs": [
    {
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       "<p>25473727 rows × 7 columns</p>\n",
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       "                MarkerName Allele1 Allele2  Effect  StdErr       P-value  \\\n",
       "0                rs7400289       t       c -0.2852  0.0525  5.491000e-08   \n",
       "1               rs75117028       a       c -0.3974  0.0744  9.088000e-08   \n",
       "2         chr13_70628410_D       d      i5  0.6437  0.1215  1.163000e-07   \n",
       "3              rs149585529       a       g  0.6425  0.1215  1.242000e-07   \n",
       "4              rs139558732       t       c  0.7161  0.1357  1.305000e-07   \n",
       "...                    ...     ...     ...     ...     ...           ...   \n",
       "25473722         rs9962851       c       g  0.0000  0.0262  1.000000e+00   \n",
       "25473723         rs9963321       t       c  0.0000  0.0965  1.000000e+00   \n",
       "25473724         rs9973857       t       c  0.0000  0.0267  1.000000e+00   \n",
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       "\n",
       "                    Direction  \n",
       "0         +------?-+-----?+--  \n",
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       "2         ?????????-+++++??+-  \n",
       "3         ?????????-+++++??+-  \n",
       "4         ??????????+++++??+-  \n",
       "...                       ...  \n",
       "25473722  +--+-+++-+++----++-  \n",
       "25473723  ?????????----+-+?+-  \n",
       "25473724  -++-+++--------++-+  \n",
       "25473725  ---++-+?+++-+--?-+-  \n",
       "25473726  -+--++-?-+--++-?--+  \n",
       "\n",
       "[25473727 rows x 7 columns]"
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     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "opposite-engagement",
   "metadata": {},
   "outputs": [],
   "source": [
    "ptsd_df_filt= ptsd_df.loc[ptsd_df['P-value']<=5e-7]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "pressing-method",
   "metadata": {},
   "outputs": [
    {
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       "      <td>-0.4419</td>\n",
       "      <td>0.0854</td>\n",
       "      <td>2.263000e-07</td>\n",
       "      <td>?????????------??-+</td>\n",
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       "      <th>8</th>\n",
       "      <td>rs6673056</td>\n",
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       "      <td>g</td>\n",
       "      <td>0.4410</td>\n",
       "      <td>0.0853</td>\n",
       "      <td>2.370000e-07</td>\n",
       "      <td>?????????++++++??+-</td>\n",
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       "      <th>9</th>\n",
       "      <td>chr1_182409244_D</td>\n",
       "      <td>d</td>\n",
       "      <td>i4</td>\n",
       "      <td>0.5358</td>\n",
       "      <td>0.1048</td>\n",
       "      <td>3.166000e-07</td>\n",
       "      <td>+++++++??+++++-?+--</td>\n",
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       "      <th>10</th>\n",
       "      <td>rs138517393</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>1.0194</td>\n",
       "      <td>0.1999</td>\n",
       "      <td>3.411000e-07</td>\n",
       "      <td>++++++-????????????</td>\n",
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       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>rs139069151</td>\n",
       "      <td>a</td>\n",
       "      <td>c</td>\n",
       "      <td>0.6037</td>\n",
       "      <td>0.1186</td>\n",
       "      <td>3.543000e-07</td>\n",
       "      <td>?????????-+++++??+-</td>\n",
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       "      <th>12</th>\n",
       "      <td>rs78664956</td>\n",
       "      <td>t</td>\n",
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       "      <td>-0.5192</td>\n",
       "      <td>0.1020</td>\n",
       "      <td>3.584000e-07</td>\n",
       "      <td>?????????------??-+</td>\n",
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       "          MarkerName Allele1 Allele2  Effect  StdErr       P-value  \\\n",
       "0          rs7400289       t       c -0.2852  0.0525  5.491000e-08   \n",
       "1         rs75117028       a       c -0.3974  0.0744  9.088000e-08   \n",
       "2   chr13_70628410_D       d      i5  0.6437  0.1215  1.163000e-07   \n",
       "3        rs149585529       a       g  0.6425  0.1215  1.242000e-07   \n",
       "4        rs139558732       t       c  0.7161  0.1357  1.305000e-07   \n",
       "5        rs190485314       t       c -2.5951  0.5007  2.189000e-07   \n",
       "6         rs75169709       t       c -0.4419  0.0854  2.262000e-07   \n",
       "7         rs78516857       a       g -0.4419  0.0854  2.263000e-07   \n",
       "8          rs6673056       t       g  0.4410  0.0853  2.370000e-07   \n",
       "9   chr1_182409244_D       d      i4  0.5358  0.1048  3.166000e-07   \n",
       "10       rs138517393       t       c  1.0194  0.1999  3.411000e-07   \n",
       "11       rs139069151       a       c  0.6037  0.1186  3.543000e-07   \n",
       "12        rs78664956       t       c -0.5192  0.1020  3.584000e-07   \n",
       "13       rs137980833       t       c  1.0803  0.2141  4.506000e-07   \n",
       "\n",
       "              Direction  \n",
       "0   +------?-+-----?+--  \n",
       "1   +------?--+----?+++  \n",
       "2   ?????????-+++++??+-  \n",
       "3   ?????????-+++++??+-  \n",
       "4   ??????????+++++??+-  \n",
       "5   -???????????????-??  \n",
       "6   ?????????------??-+  \n",
       "7   ?????????------??-+  \n",
       "8   ?????????++++++??+-  \n",
       "9   +++++++??+++++-?+--  \n",
       "10  ++++++-????????????  \n",
       "11  ?????????-+++++??+-  \n",
       "12  ?????????------??-+  \n",
       "13  ?????????-+?+++??++  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_df_filt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "alternate-steal",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "<ipython-input-8-9b395ebc31fe>:3: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  ptsd_df_filt['Possible Odds Ratio']= ptsd_df_filt.apply(lambda x: math.exp(x['Effect']), axis=1)\n"
     ]
    }
   ],
   "source": [
    "import math\n",
    "\n",
    "ptsd_df_filt['Possible Odds Ratio']= ptsd_df_filt.apply(lambda x: math.exp(x['Effect']), axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "original-triple",
   "metadata": {},
   "outputs": [
    {
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       "      <td>0.6425</td>\n",
       "      <td>0.1215</td>\n",
       "      <td>1.242000e-07</td>\n",
       "      <td>?????????-+++++??+-</td>\n",
       "      <td>1.901228</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>rs139558732</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>0.7161</td>\n",
       "      <td>0.1357</td>\n",
       "      <td>1.305000e-07</td>\n",
       "      <td>??????????+++++??+-</td>\n",
       "      <td>2.046437</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>rs190485314</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>-2.5951</td>\n",
       "      <td>0.5007</td>\n",
       "      <td>2.189000e-07</td>\n",
       "      <td>-???????????????-??</td>\n",
       "      <td>0.074638</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>rs75169709</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>-0.4419</td>\n",
       "      <td>0.0854</td>\n",
       "      <td>2.262000e-07</td>\n",
       "      <td>?????????------??-+</td>\n",
       "      <td>0.642814</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>rs78516857</td>\n",
       "      <td>a</td>\n",
       "      <td>g</td>\n",
       "      <td>-0.4419</td>\n",
       "      <td>0.0854</td>\n",
       "      <td>2.263000e-07</td>\n",
       "      <td>?????????------??-+</td>\n",
       "      <td>0.642814</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>rs6673056</td>\n",
       "      <td>t</td>\n",
       "      <td>g</td>\n",
       "      <td>0.4410</td>\n",
       "      <td>0.0853</td>\n",
       "      <td>2.370000e-07</td>\n",
       "      <td>?????????++++++??+-</td>\n",
       "      <td>1.554261</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>chr1_182409244_D</td>\n",
       "      <td>d</td>\n",
       "      <td>i4</td>\n",
       "      <td>0.5358</td>\n",
       "      <td>0.1048</td>\n",
       "      <td>3.166000e-07</td>\n",
       "      <td>+++++++??+++++-?+--</td>\n",
       "      <td>1.708815</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>rs138517393</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>1.0194</td>\n",
       "      <td>0.1999</td>\n",
       "      <td>3.411000e-07</td>\n",
       "      <td>++++++-????????????</td>\n",
       "      <td>2.771531</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>rs139069151</td>\n",
       "      <td>a</td>\n",
       "      <td>c</td>\n",
       "      <td>0.6037</td>\n",
       "      <td>0.1186</td>\n",
       "      <td>3.543000e-07</td>\n",
       "      <td>?????????-+++++??+-</td>\n",
       "      <td>1.828873</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>rs78664956</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>-0.5192</td>\n",
       "      <td>0.1020</td>\n",
       "      <td>3.584000e-07</td>\n",
       "      <td>?????????------??-+</td>\n",
       "      <td>0.594996</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>rs137980833</td>\n",
       "      <td>t</td>\n",
       "      <td>c</td>\n",
       "      <td>1.0803</td>\n",
       "      <td>0.2141</td>\n",
       "      <td>4.506000e-07</td>\n",
       "      <td>?????????-+?+++??++</td>\n",
       "      <td>2.945563</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          MarkerName Allele1 Allele2  Effect  StdErr       P-value  \\\n",
       "0          rs7400289       t       c -0.2852  0.0525  5.491000e-08   \n",
       "1         rs75117028       a       c -0.3974  0.0744  9.088000e-08   \n",
       "2   chr13_70628410_D       d      i5  0.6437  0.1215  1.163000e-07   \n",
       "3        rs149585529       a       g  0.6425  0.1215  1.242000e-07   \n",
       "4        rs139558732       t       c  0.7161  0.1357  1.305000e-07   \n",
       "5        rs190485314       t       c -2.5951  0.5007  2.189000e-07   \n",
       "6         rs75169709       t       c -0.4419  0.0854  2.262000e-07   \n",
       "7         rs78516857       a       g -0.4419  0.0854  2.263000e-07   \n",
       "8          rs6673056       t       g  0.4410  0.0853  2.370000e-07   \n",
       "9   chr1_182409244_D       d      i4  0.5358  0.1048  3.166000e-07   \n",
       "10       rs138517393       t       c  1.0194  0.1999  3.411000e-07   \n",
       "11       rs139069151       a       c  0.6037  0.1186  3.543000e-07   \n",
       "12        rs78664956       t       c -0.5192  0.1020  3.584000e-07   \n",
       "13       rs137980833       t       c  1.0803  0.2141  4.506000e-07   \n",
       "\n",
       "              Direction  Possible Odds Ratio  \n",
       "0   +------?-+-----?+--             0.751864  \n",
       "1   +------?--+----?+++             0.672065  \n",
       "2   ?????????-+++++??+-             1.903511  \n",
       "3   ?????????-+++++??+-             1.901228  \n",
       "4   ??????????+++++??+-             2.046437  \n",
       "5   -???????????????-??             0.074638  \n",
       "6   ?????????------??-+             0.642814  \n",
       "7   ?????????------??-+             0.642814  \n",
       "8   ?????????++++++??+-             1.554261  \n",
       "9   +++++++??+++++-?+--             1.708815  \n",
       "10  ++++++-????????????             2.771531  \n",
       "11  ?????????-+++++??+-             1.828873  \n",
       "12  ?????????------??-+             0.594996  \n",
       "13  ?????????-+?+++??++             2.945563  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ptsd_df_filt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "id": "cooked-keyboard",
   "metadata": {},
   "outputs": [],
   "source": [
    "schizophrenia_df = pd.read_csv(\"daner_natgen_eas_eur_autosomes\", sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "muslim-statement",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>FRQ_A_56418</th>\n",
       "      <th>FRQ_U_78818</th>\n",
       "      <th>INFO</th>\n",
       "      <th>OR</th>\n",
       "      <th>SE</th>\n",
       "      <th>P</th>\n",
       "      <th>ngt</th>\n",
       "      <th>Direction</th>\n",
       "      <th>HetISqt</th>\n",
       "      <th>HetDf</th>\n",
       "      <th>HetPVa</th>\n",
       "      <th>Nca</th>\n",
       "      <th>Nco</th>\n",
       "      <th>Neff</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>8</td>\n",
       "      <td>rs62513865</td>\n",
       "      <td>101592213</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0716</td>\n",
       "      <td>0.0750</td>\n",
       "      <td>0.956</td>\n",
       "      <td>0.98167</td>\n",
       "      <td>0.0213</td>\n",
       "      <td>0.38510</td>\n",
       "      <td>0</td>\n",
       "      <td>-???????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.0000</td>\n",
       "      <td>33640</td>\n",
       "      <td>43456</td>\n",
       "      <td>37923.10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>8</td>\n",
       "      <td>rs73696507</td>\n",
       "      <td>105231413</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.9590</td>\n",
       "      <td>0.9600</td>\n",
       "      <td>0.998</td>\n",
       "      <td>1.00975</td>\n",
       "      <td>0.0426</td>\n",
       "      <td>0.82000</td>\n",
       "      <td>0</td>\n",
       "      <td>++--????</td>\n",
       "      <td>3.9</td>\n",
       "      <td>3</td>\n",
       "      <td>0.3733</td>\n",
       "      <td>14583</td>\n",
       "      <td>17261</td>\n",
       "      <td>15712.17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>8</td>\n",
       "      <td>rs79643588</td>\n",
       "      <td>106973048</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0713</td>\n",
       "      <td>0.0743</td>\n",
       "      <td>0.990</td>\n",
       "      <td>0.98531</td>\n",
       "      <td>0.0185</td>\n",
       "      <td>0.42370</td>\n",
       "      <td>0</td>\n",
       "      <td>-???????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.0000</td>\n",
       "      <td>46945</td>\n",
       "      <td>59700</td>\n",
       "      <td>52551.45</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>8</td>\n",
       "      <td>rs6994300</td>\n",
       "      <td>102569817</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0666</td>\n",
       "      <td>0.0664</td>\n",
       "      <td>0.878</td>\n",
       "      <td>0.99392</td>\n",
       "      <td>0.0373</td>\n",
       "      <td>0.86990</td>\n",
       "      <td>0</td>\n",
       "      <td>---+????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.5146</td>\n",
       "      <td>14583</td>\n",
       "      <td>17261</td>\n",
       "      <td>15712.17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>8</td>\n",
       "      <td>rs17396518</td>\n",
       "      <td>108690829</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.4890</td>\n",
       "      <td>0.4910</td>\n",
       "      <td>0.981</td>\n",
       "      <td>1.00682</td>\n",
       "      <td>0.0094</td>\n",
       "      <td>0.47210</td>\n",
       "      <td>16</td>\n",
       "      <td>++++????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.4339</td>\n",
       "      <td>48223</td>\n",
       "      <td>60717</td>\n",
       "      <td>53635.28</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13558618</th>\n",
       "      <td>20</td>\n",
       "      <td>rs148755306</td>\n",
       "      <td>47231076</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0154</td>\n",
       "      <td>0.0221</td>\n",
       "      <td>0.869</td>\n",
       "      <td>0.63021</td>\n",
       "      <td>0.3471</td>\n",
       "      <td>0.18350</td>\n",
       "      <td>0</td>\n",
       "      <td>-???????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.0000</td>\n",
       "      <td>13305</td>\n",
       "      <td>16244</td>\n",
       "      <td>14628.34</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13558619</th>\n",
       "      <td>20</td>\n",
       "      <td>rs117705259</td>\n",
       "      <td>46761380</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.0154</td>\n",
       "      <td>0.0152</td>\n",
       "      <td>0.968</td>\n",
       "      <td>1.02655</td>\n",
       "      <td>0.0463</td>\n",
       "      <td>0.57140</td>\n",
       "      <td>0</td>\n",
       "      <td>+???????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.0000</td>\n",
       "      <td>33640</td>\n",
       "      <td>43456</td>\n",
       "      <td>37923.10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13558620</th>\n",
       "      <td>20</td>\n",
       "      <td>rs6017602</td>\n",
       "      <td>44168957</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.0432</td>\n",
       "      <td>0.0396</td>\n",
       "      <td>0.995</td>\n",
       "      <td>1.09385</td>\n",
       "      <td>0.0425</td>\n",
       "      <td>0.03472</td>\n",
       "      <td>5</td>\n",
       "      <td>++--????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.6503</td>\n",
       "      <td>14583</td>\n",
       "      <td>17261</td>\n",
       "      <td>15712.17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13558621</th>\n",
       "      <td>20</td>\n",
       "      <td>rs144166091</td>\n",
       "      <td>45724327</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.9860</td>\n",
       "      <td>0.9870</td>\n",
       "      <td>0.804</td>\n",
       "      <td>0.96435</td>\n",
       "      <td>0.0536</td>\n",
       "      <td>0.49820</td>\n",
       "      <td>0</td>\n",
       "      <td>-???????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.0000</td>\n",
       "      <td>33640</td>\n",
       "      <td>43456</td>\n",
       "      <td>37923.10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13558622</th>\n",
       "      <td>20</td>\n",
       "      <td>rs1111021</td>\n",
       "      <td>42747689</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.2790</td>\n",
       "      <td>0.2810</td>\n",
       "      <td>0.982</td>\n",
       "      <td>0.99233</td>\n",
       "      <td>0.0103</td>\n",
       "      <td>0.45640</td>\n",
       "      <td>1</td>\n",
       "      <td>-++-????</td>\n",
       "      <td>24.5</td>\n",
       "      <td>3</td>\n",
       "      <td>0.2644</td>\n",
       "      <td>48223</td>\n",
       "      <td>60717</td>\n",
       "      <td>53635.28</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>13558623 rows × 19 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          CHR          SNP         BP A1 A2  FRQ_A_56418  FRQ_U_78818   INFO  \\\n",
       "0           8   rs62513865  101592213  T  C       0.0716       0.0750  0.956   \n",
       "1           8   rs73696507  105231413  T  C       0.9590       0.9600  0.998   \n",
       "2           8   rs79643588  106973048  A  G       0.0713       0.0743  0.990   \n",
       "3           8    rs6994300  102569817  A  G       0.0666       0.0664  0.878   \n",
       "4           8   rs17396518  108690829  T  G       0.4890       0.4910  0.981   \n",
       "...       ...          ...        ... .. ..          ...          ...    ...   \n",
       "13558618   20  rs148755306   47231076  A  G       0.0154       0.0221  0.869   \n",
       "13558619   20  rs117705259   46761380  A  G       0.0154       0.0152  0.968   \n",
       "13558620   20    rs6017602   44168957  T  C       0.0432       0.0396  0.995   \n",
       "13558621   20  rs144166091   45724327  T  C       0.9860       0.9870  0.804   \n",
       "13558622   20    rs1111021   42747689  T  C       0.2790       0.2810  0.982   \n",
       "\n",
       "               OR      SE        P  ngt Direction  HetISqt  HetDf  HetPVa  \\\n",
       "0         0.98167  0.0213  0.38510    0  -???????      0.0      0  1.0000   \n",
       "1         1.00975  0.0426  0.82000    0  ++--????      3.9      3  0.3733   \n",
       "2         0.98531  0.0185  0.42370    0  -???????      0.0      0  1.0000   \n",
       "3         0.99392  0.0373  0.86990    0  ---+????      0.0      3  0.5146   \n",
       "4         1.00682  0.0094  0.47210   16  ++++????      0.0      3  0.4339   \n",
       "...           ...     ...      ...  ...       ...      ...    ...     ...   \n",
       "13558618  0.63021  0.3471  0.18350    0  -???????      0.0      0  1.0000   \n",
       "13558619  1.02655  0.0463  0.57140    0  +???????      0.0      0  1.0000   \n",
       "13558620  1.09385  0.0425  0.03472    5  ++--????      0.0      3  0.6503   \n",
       "13558621  0.96435  0.0536  0.49820    0  -???????      0.0      0  1.0000   \n",
       "13558622  0.99233  0.0103  0.45640    1  -++-????     24.5      3  0.2644   \n",
       "\n",
       "            Nca    Nco      Neff  \n",
       "0         33640  43456  37923.10  \n",
       "1         14583  17261  15712.17  \n",
       "2         46945  59700  52551.45  \n",
       "3         14583  17261  15712.17  \n",
       "4         48223  60717  53635.28  \n",
       "...         ...    ...       ...  \n",
       "13558618  13305  16244  14628.34  \n",
       "13558619  33640  43456  37923.10  \n",
       "13558620  14583  17261  15712.17  \n",
       "13558621  33640  43456  37923.10  \n",
       "13558622  48223  60717  53635.28  \n",
       "\n",
       "[13558623 rows x 19 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizophrenia_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "effective-remark",
   "metadata": {},
   "outputs": [
    {
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      "text/plain": [
       "          CHR           SNP         BP  A1 A2  FRQ_A_56418  FRQ_U_78818  \\\n",
       "10893042    5  rs139936287m   65608563  GA  G       0.7550       0.7520   \n",
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       "...       ...           ...        ...  .. ..          ...          ...   \n",
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       "4553055     6     rs1233578   28712247   A  G       0.9030       0.8910   \n",
       "4587237     6     rs9257566   29144532   T  C       0.0685       0.0811   \n",
       "\n",
       "           INFO       OR      SE             P  ngt Direction  HetISqt  HetDf  \\\n",
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       "6069878   0.998  1.00000  0.0340  1.000000e+00   13  0???????      0.0      0   \n",
       "5186828   0.956  1.00000  0.0302  1.000000e+00    0  0???????      0.0      0   \n",
       "1910020   0.883  1.00000  0.0289  1.000000e+00    0  0???????      0.0      0   \n",
       "...         ...      ...     ...           ...  ...       ...      ...    ...   \n",
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       "4597781   1.010  1.24222  0.0198  6.319000e-28    1  +???????      0.0      0   \n",
       "4535270   1.010  0.80413  0.0198  3.427000e-28   27  -???????      0.0      0   \n",
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       "\n",
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       "...           ...    ...    ...       ...  \n",
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       "\n",
       "[13558623 rows x 19 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizophrenia_df.sort_values('P',ascending= False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "corporate-origin",
   "metadata": {},
   "outputs": [],
   "source": [
    "schizo_df_filt= schizophrenia_df.loc[schizophrenia_df['P']<=5e-8]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "lonely-romance",
   "metadata": {},
   "outputs": [
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       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>100535</th>\n",
       "      <td>16</td>\n",
       "      <td>rs9933980</td>\n",
       "      <td>64370514</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.356</td>\n",
       "      <td>0.396</td>\n",
       "      <td>0.957</td>\n",
       "      <td>0.94810</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>2.986000e-09</td>\n",
       "      <td>1</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>65.8</td>\n",
       "      <td>7</td>\n",
       "      <td>0.004638</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13394708</th>\n",
       "      <td>2</td>\n",
       "      <td>rs3736594</td>\n",
       "      <td>27995781</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.380</td>\n",
       "      <td>0.386</td>\n",
       "      <td>0.964</td>\n",
       "      <td>0.94667</td>\n",
       "      <td>0.0093</td>\n",
       "      <td>3.374000e-09</td>\n",
       "      <td>30</td>\n",
       "      <td>----+---</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.682300</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13531911</th>\n",
       "      <td>20</td>\n",
       "      <td>rs495146</td>\n",
       "      <td>48130328</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.303</td>\n",
       "      <td>0.341</td>\n",
       "      <td>0.961</td>\n",
       "      <td>1.05496</td>\n",
       "      <td>0.0098</td>\n",
       "      <td>4.319000e-08</td>\n",
       "      <td>38</td>\n",
       "      <td>++++--++</td>\n",
       "      <td>28.6</td>\n",
       "      <td>7</td>\n",
       "      <td>0.200200</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13534498</th>\n",
       "      <td>20</td>\n",
       "      <td>rs7267348</td>\n",
       "      <td>48131036</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.703</td>\n",
       "      <td>0.663</td>\n",
       "      <td>0.961</td>\n",
       "      <td>0.94734</td>\n",
       "      <td>0.0099</td>\n",
       "      <td>3.981000e-08</td>\n",
       "      <td>1</td>\n",
       "      <td>----++--</td>\n",
       "      <td>32.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.172800</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13535893</th>\n",
       "      <td>20</td>\n",
       "      <td>rs6019879</td>\n",
       "      <td>48130628</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.703</td>\n",
       "      <td>0.663</td>\n",
       "      <td>0.961</td>\n",
       "      <td>0.94753</td>\n",
       "      <td>0.0098</td>\n",
       "      <td>4.526000e-08</td>\n",
       "      <td>18</td>\n",
       "      <td>----++--</td>\n",
       "      <td>32.2</td>\n",
       "      <td>7</td>\n",
       "      <td>0.170600</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13537154</th>\n",
       "      <td>20</td>\n",
       "      <td>rs7271624</td>\n",
       "      <td>48129169</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>0.741</td>\n",
       "      <td>0.753</td>\n",
       "      <td>0.997</td>\n",
       "      <td>0.94374</td>\n",
       "      <td>0.0105</td>\n",
       "      <td>3.416000e-08</td>\n",
       "      <td>20</td>\n",
       "      <td>----????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.809700</td>\n",
       "      <td>48223</td>\n",
       "      <td>60717</td>\n",
       "      <td>53635.28</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>15445 rows × 19 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          CHR         SNP         BP A1 A2  FRQ_A_56418  FRQ_U_78818   INFO  \\\n",
       "379         8   rs1434281  103671080  A  G        0.344        0.399  0.957   \n",
       "42353       8   rs4734654  103669991  A  G        0.656        0.601  0.959   \n",
       "99597      16   rs4949087   64333546  A  G        0.354        0.393  0.958   \n",
       "99851      16  rs34707355   64375453  T  C        0.357        0.396  0.954   \n",
       "100535     16   rs9933980   64370514  T  G        0.356        0.396  0.957   \n",
       "...       ...         ...        ... .. ..          ...          ...    ...   \n",
       "13394708    2   rs3736594   27995781  A  C        0.380        0.386  0.964   \n",
       "13531911   20    rs495146   48130328  T  C        0.303        0.341  0.961   \n",
       "13534498   20   rs7267348   48131036  T  C        0.703        0.663  0.961   \n",
       "13535893   20   rs6019879   48130628  T  C        0.703        0.663  0.961   \n",
       "13537154   20   rs7271624   48129169  C  G        0.741        0.753  0.997   \n",
       "\n",
       "               OR      SE             P  ngt Direction  HetISqt  HetDf  \\\n",
       "379       0.94810  0.0095  1.705000e-08    0  -+----+-      0.0      7   \n",
       "42353     1.05443  0.0094  1.503000e-08   24  +-++++-+      0.0      7   \n",
       "99597     0.95037  0.0090  1.372000e-08    0  --+-++--     64.7      7   \n",
       "99851     0.94743  0.0092  5.164000e-09    0  --+-++--     67.4      7   \n",
       "100535    0.94810  0.0090  2.986000e-09    1  --+-++--     65.8      7   \n",
       "...           ...     ...           ...  ...       ...      ...    ...   \n",
       "13394708  0.94667  0.0093  3.374000e-09   30  ----+---      0.0      7   \n",
       "13531911  1.05496  0.0098  4.319000e-08   38  ++++--++     28.6      7   \n",
       "13534498  0.94734  0.0099  3.981000e-08    1  ----++--     32.0      7   \n",
       "13535893  0.94753  0.0098  4.526000e-08   18  ----++--     32.2      7   \n",
       "13537154  0.94374  0.0105  3.416000e-08   20  ----????      0.0      3   \n",
       "\n",
       "            HetPVa    Nca    Nco      Neff  \n",
       "379       0.573300  56418  78818  64441.44  \n",
       "42353     0.566500  56418  78818  64441.44  \n",
       "99597     0.005922  56418  78818  64441.44  \n",
       "99851     0.003126  56418  78818  64441.44  \n",
       "100535    0.004638  56418  78818  64441.44  \n",
       "...            ...    ...    ...       ...  \n",
       "13394708  0.682300  56418  78818  64441.44  \n",
       "13531911  0.200200  56418  78818  64441.44  \n",
       "13534498  0.172800  56418  78818  64441.44  \n",
       "13535893  0.170600  56418  78818  64441.44  \n",
       "13537154  0.809700  48223  60717  53635.28  \n",
       "\n",
       "[15445 rows x 19 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizo_df_filt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "virgin-liechtenstein",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>FRQ_A_56418</th>\n",
       "      <th>FRQ_U_78818</th>\n",
       "      <th>INFO</th>\n",
       "      <th>OR</th>\n",
       "      <th>SE</th>\n",
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       "      <th>ngt</th>\n",
       "      <th>Direction</th>\n",
       "      <th>HetISqt</th>\n",
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       "      <td>chr6:26518757</td>\n",
       "      <td>26518757</td>\n",
       "      <td>A</td>\n",
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       "      <td>2.623000e-13</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>4802236</th>\n",
       "      <td>6</td>\n",
       "      <td>chr6:30332254</td>\n",
       "      <td>30332254</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.97300</td>\n",
       "      <td>0.9700</td>\n",
       "      <td>0.481</td>\n",
       "      <td>1.37355</td>\n",
       "      <td>0.0465</td>\n",
       "      <td>8.745000e-12</td>\n",
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       "      <td>1.0</td>\n",
       "      <td>33640</td>\n",
       "      <td>43456</td>\n",
       "      <td>37923.10</td>\n",
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       "    <tr>\n",
       "      <th>4565589</th>\n",
       "      <td>6</td>\n",
       "      <td>rs71559051</td>\n",
       "      <td>27799470</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.94500</td>\n",
       "      <td>0.9350</td>\n",
       "      <td>0.758</td>\n",
       "      <td>1.30918</td>\n",
       "      <td>0.0263</td>\n",
       "      <td>1.267000e-24</td>\n",
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       "    <tr>\n",
       "      <th>4559282</th>\n",
       "      <td>6</td>\n",
       "      <td>rs113780580</td>\n",
       "      <td>27555056</td>\n",
       "      <td>A</td>\n",
       "      <td>AACAC</td>\n",
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       "    <tr>\n",
       "      <th>4553584</th>\n",
       "      <td>6</td>\n",
       "      <td>rs71557345</td>\n",
       "      <td>26680698</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
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       "      <td>0.0734</td>\n",
       "      <td>0.903</td>\n",
       "      <td>0.78671</td>\n",
       "      <td>0.0229</td>\n",
       "      <td>1.116000e-25</td>\n",
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       "    <tr>\n",
       "      <th>4537686</th>\n",
       "      <td>6</td>\n",
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       "      <td>27729706</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
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       "      <td>0.0756</td>\n",
       "      <td>0.866</td>\n",
       "      <td>0.78568</td>\n",
       "      <td>0.0230</td>\n",
       "      <td>9.891000e-26</td>\n",
       "      <td>0</td>\n",
       "      <td>-???????</td>\n",
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       "      <td>0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>33640</td>\n",
       "      <td>43456</td>\n",
       "      <td>37923.10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4543692</th>\n",
       "      <td>6</td>\n",
       "      <td>rs35202262</td>\n",
       "      <td>27799514</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.06460</td>\n",
       "      <td>0.0766</td>\n",
       "      <td>0.882</td>\n",
       "      <td>0.78553</td>\n",
       "      <td>0.0227</td>\n",
       "      <td>2.066000e-26</td>\n",
       "      <td>0</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>4597569</th>\n",
       "      <td>6</td>\n",
       "      <td>chr6:27244243</td>\n",
       "      <td>27244243</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.02760</td>\n",
       "      <td>0.0311</td>\n",
       "      <td>0.475</td>\n",
       "      <td>0.75828</td>\n",
       "      <td>0.0432</td>\n",
       "      <td>1.502000e-10</td>\n",
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       "      <td>-???????</td>\n",
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       "      <td>0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>46945</td>\n",
       "      <td>59700</td>\n",
       "      <td>52551.45</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4763487</th>\n",
       "      <td>6</td>\n",
       "      <td>rs114486118</td>\n",
       "      <td>30346826</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.00894</td>\n",
       "      <td>0.0104</td>\n",
       "      <td>0.235</td>\n",
       "      <td>0.50535</td>\n",
       "      <td>0.1221</td>\n",
       "      <td>2.274000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>-???????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>33640</td>\n",
       "      <td>43456</td>\n",
       "      <td>37923.10</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>15445 rows × 19 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         CHR            SNP        BP A1     A2  FRQ_A_56418  FRQ_U_78818  \\\n",
       "4553688    6  chr6:26518757  26518757  A      T      0.99300       0.9910   \n",
       "4584146    6    rs114476648  27633802  T      C      0.98100       0.9790   \n",
       "4802236    6  chr6:30332254  30332254  T      C      0.97300       0.9700   \n",
       "4565589    6     rs71559051  27799470  A      G      0.94500       0.9350   \n",
       "4559282    6    rs113780580  27555056  A  AACAC      0.94100       0.9300   \n",
       "...      ...            ...       ... ..    ...          ...          ...   \n",
       "4553584    6     rs71557345  26680698  A      G      0.06170       0.0734   \n",
       "4537686    6    rs192804591  27729706  A      T      0.06370       0.0756   \n",
       "4543692    6     rs35202262  27799514  T      C      0.06460       0.0766   \n",
       "4597569    6  chr6:27244243  27244243  T      C      0.02760       0.0311   \n",
       "4763487    6    rs114486118  30346826  T      C      0.00894       0.0104   \n",
       "\n",
       "          INFO       OR      SE             P  ngt Direction  HetISqt  HetDf  \\\n",
       "4553688  0.442  1.78229  0.1005  8.912000e-09    0  +???????      0.0      0   \n",
       "4584146  0.446  1.50606  0.0560  2.623000e-13    0  +???????      0.0      0   \n",
       "4802236  0.481  1.37355  0.0465  8.745000e-12    0  +???????      0.0      0   \n",
       "4565589  0.758  1.30918  0.0263  1.267000e-24    0  +???????      0.0      0   \n",
       "4559282  0.861  1.27813  0.0240  1.534000e-24    0  +???????      0.0      0   \n",
       "...        ...      ...     ...           ...  ...       ...      ...    ...   \n",
       "4553584  0.903  0.78671  0.0229  1.116000e-25    0  -???????      0.0      0   \n",
       "4537686  0.866  0.78568  0.0230  9.891000e-26    0  -???????      0.0      0   \n",
       "4543692  0.882  0.78553  0.0227  2.066000e-26    0  -???????      0.0      0   \n",
       "4597569  0.475  0.75828  0.0432  1.502000e-10    0  -???????      0.0      0   \n",
       "4763487  0.235  0.50535  0.1221  2.274000e-08    0  -???????      0.0      0   \n",
       "\n",
       "         HetPVa    Nca    Nco      Neff  \n",
       "4553688     1.0  33640  43456  37923.10  \n",
       "4584146     1.0  46945  59700  52551.45  \n",
       "4802236     1.0  33640  43456  37923.10  \n",
       "4565589     1.0  33640  43456  37923.10  \n",
       "4559282     1.0  33640  43456  37923.10  \n",
       "...         ...    ...    ...       ...  \n",
       "4553584     1.0  33640  43456  37923.10  \n",
       "4537686     1.0  33640  43456  37923.10  \n",
       "4543692     1.0  33640  43456  37923.10  \n",
       "4597569     1.0  46945  59700  52551.45  \n",
       "4763487     1.0  33640  43456  37923.10  \n",
       "\n",
       "[15445 rows x 19 columns]"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizo_df_filt.sort_values('OR',ascending= False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "cardiac-surge",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>FRQ_A_56418</th>\n",
       "      <th>FRQ_U_78818</th>\n",
       "      <th>INFO</th>\n",
       "      <th>OR</th>\n",
       "      <th>SE</th>\n",
       "      <th>P</th>\n",
       "      <th>ngt</th>\n",
       "      <th>Direction</th>\n",
       "      <th>HetISqt</th>\n",
       "      <th>HetDf</th>\n",
       "      <th>HetPVa</th>\n",
       "      <th>Nca</th>\n",
       "      <th>Nco</th>\n",
       "      <th>Neff</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>379</th>\n",
       "      <td>8</td>\n",
       "      <td>rs1434281</td>\n",
       "      <td>103671080</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
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       "      <td>0.0095</td>\n",
       "      <td>1.705000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>-+----+-</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.573300</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
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       "    <tr>\n",
       "      <th>42353</th>\n",
       "      <td>8</td>\n",
       "      <td>rs4734654</td>\n",
       "      <td>103669991</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.656</td>\n",
       "      <td>0.601</td>\n",
       "      <td>0.959</td>\n",
       "      <td>1.05443</td>\n",
       "      <td>0.0094</td>\n",
       "      <td>1.503000e-08</td>\n",
       "      <td>24</td>\n",
       "      <td>+-++++-+</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.566500</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
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       "    <tr>\n",
       "      <th>99597</th>\n",
       "      <td>16</td>\n",
       "      <td>rs4949087</td>\n",
       "      <td>64333546</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.354</td>\n",
       "      <td>0.393</td>\n",
       "      <td>0.958</td>\n",
       "      <td>0.95037</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>1.372000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>64.7</td>\n",
       "      <td>7</td>\n",
       "      <td>0.005922</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99851</th>\n",
       "      <td>16</td>\n",
       "      <td>rs34707355</td>\n",
       "      <td>64375453</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.357</td>\n",
       "      <td>0.396</td>\n",
       "      <td>0.954</td>\n",
       "      <td>0.94743</td>\n",
       "      <td>0.0092</td>\n",
       "      <td>5.164000e-09</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>67.4</td>\n",
       "      <td>7</td>\n",
       "      <td>0.003126</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>100535</th>\n",
       "      <td>16</td>\n",
       "      <td>rs9933980</td>\n",
       "      <td>64370514</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.356</td>\n",
       "      <td>0.396</td>\n",
       "      <td>0.957</td>\n",
       "      <td>0.94810</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>2.986000e-09</td>\n",
       "      <td>1</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>65.8</td>\n",
       "      <td>7</td>\n",
       "      <td>0.004638</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101159</th>\n",
       "      <td>16</td>\n",
       "      <td>rs9934855</td>\n",
       "      <td>64326532</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.646</td>\n",
       "      <td>0.607</td>\n",
       "      <td>0.957</td>\n",
       "      <td>1.05243</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>1.285000e-08</td>\n",
       "      <td>15</td>\n",
       "      <td>++-+--++</td>\n",
       "      <td>63.4</td>\n",
       "      <td>7</td>\n",
       "      <td>0.007763</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101491</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2917691</td>\n",
       "      <td>64297994</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.570</td>\n",
       "      <td>0.553</td>\n",
       "      <td>0.959</td>\n",
       "      <td>1.04970</td>\n",
       "      <td>0.0086</td>\n",
       "      <td>1.634000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>++-+---+</td>\n",
       "      <td>66.8</td>\n",
       "      <td>7</td>\n",
       "      <td>0.003610</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101607</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2917690</td>\n",
       "      <td>64297917</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.428</td>\n",
       "      <td>0.445</td>\n",
       "      <td>0.956</td>\n",
       "      <td>0.95266</td>\n",
       "      <td>0.0086</td>\n",
       "      <td>1.713000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-+++-</td>\n",
       "      <td>65.9</td>\n",
       "      <td>7</td>\n",
       "      <td>0.004527</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101648</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2917695</td>\n",
       "      <td>64299409</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>0.584</td>\n",
       "      <td>0.571</td>\n",
       "      <td>0.995</td>\n",
       "      <td>1.05232</td>\n",
       "      <td>0.0093</td>\n",
       "      <td>4.129000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>++-+????</td>\n",
       "      <td>69.2</td>\n",
       "      <td>3</td>\n",
       "      <td>0.020900</td>\n",
       "      <td>48223</td>\n",
       "      <td>60717</td>\n",
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       "    <tr>\n",
       "      <th>102242</th>\n",
       "      <td>16</td>\n",
       "      <td>rs11643828</td>\n",
       "      <td>64349345</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>0.325</td>\n",
       "      <td>0.339</td>\n",
       "      <td>0.994</td>\n",
       "      <td>0.94374</td>\n",
       "      <td>0.0097</td>\n",
       "      <td>2.437000e-09</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-????</td>\n",
       "      <td>63.3</td>\n",
       "      <td>3</td>\n",
       "      <td>0.042680</td>\n",
       "      <td>48223</td>\n",
       "      <td>60717</td>\n",
       "      <td>53635.28</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103280</th>\n",
       "      <td>16</td>\n",
       "      <td>rs12930453</td>\n",
       "      <td>64315466</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>0.322</td>\n",
       "      <td>0.335</td>\n",
       "      <td>0.990</td>\n",
       "      <td>0.94554</td>\n",
       "      <td>0.0097</td>\n",
       "      <td>8.075000e-09</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-????</td>\n",
       "      <td>62.6</td>\n",
       "      <td>3</td>\n",
       "      <td>0.045420</td>\n",
       "      <td>48223</td>\n",
       "      <td>60717</td>\n",
       "      <td>53635.28</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103838</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2917701</td>\n",
       "      <td>64302367</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>0.584</td>\n",
       "      <td>0.571</td>\n",
       "      <td>0.996</td>\n",
       "      <td>1.05211</td>\n",
       "      <td>0.0092</td>\n",
       "      <td>3.341000e-08</td>\n",
       "      <td>14</td>\n",
       "      <td>++-+????</td>\n",
       "      <td>67.6</td>\n",
       "      <td>3</td>\n",
       "      <td>0.026080</td>\n",
       "      <td>48223</td>\n",
       "      <td>60717</td>\n",
       "      <td>53635.28</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103856</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2319807</td>\n",
       "      <td>64301371</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.570</td>\n",
       "      <td>0.553</td>\n",
       "      <td>0.959</td>\n",
       "      <td>1.04938</td>\n",
       "      <td>0.0086</td>\n",
       "      <td>2.025000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>++-+---+</td>\n",
       "      <td>66.2</td>\n",
       "      <td>7</td>\n",
       "      <td>0.004236</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104002</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2917689</td>\n",
       "      <td>64297905</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.571</td>\n",
       "      <td>0.554</td>\n",
       "      <td>0.957</td>\n",
       "      <td>1.04949</td>\n",
       "      <td>0.0086</td>\n",
       "      <td>1.845000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>++-+---+</td>\n",
       "      <td>65.8</td>\n",
       "      <td>7</td>\n",
       "      <td>0.004628</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
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       "    <tr>\n",
       "      <th>104368</th>\n",
       "      <td>16</td>\n",
       "      <td>rs6498941</td>\n",
       "      <td>64329023</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.355</td>\n",
       "      <td>0.394</td>\n",
       "      <td>0.957</td>\n",
       "      <td>0.95009</td>\n",
       "      <td>0.0092</td>\n",
       "      <td>2.928000e-08</td>\n",
       "      <td>1</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>64.1</td>\n",
       "      <td>7</td>\n",
       "      <td>0.006824</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104559</th>\n",
       "      <td>16</td>\n",
       "      <td>rs9935149</td>\n",
       "      <td>64322807</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.355</td>\n",
       "      <td>0.394</td>\n",
       "      <td>0.956</td>\n",
       "      <td>0.94990</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>1.031000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>62.5</td>\n",
       "      <td>7</td>\n",
       "      <td>0.009374</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104977</th>\n",
       "      <td>16</td>\n",
       "      <td>rs4949070</td>\n",
       "      <td>64333189</td>\n",
       "      <td>C</td>\n",
       "      <td>G</td>\n",
       "      <td>0.680</td>\n",
       "      <td>0.666</td>\n",
       "      <td>0.992</td>\n",
       "      <td>1.05792</td>\n",
       "      <td>0.0098</td>\n",
       "      <td>9.411000e-09</td>\n",
       "      <td>0</td>\n",
       "      <td>++-+????</td>\n",
       "      <td>65.7</td>\n",
       "      <td>3</td>\n",
       "      <td>0.033030</td>\n",
       "      <td>48223</td>\n",
       "      <td>60717</td>\n",
       "      <td>53635.28</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105085</th>\n",
       "      <td>16</td>\n",
       "      <td>rs1837017</td>\n",
       "      <td>64298158</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.430</td>\n",
       "      <td>0.447</td>\n",
       "      <td>0.959</td>\n",
       "      <td>0.95256</td>\n",
       "      <td>0.0086</td>\n",
       "      <td>1.571000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-+++-</td>\n",
       "      <td>66.9</td>\n",
       "      <td>7</td>\n",
       "      <td>0.003515</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105567</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2967190</td>\n",
       "      <td>64298669</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.430</td>\n",
       "      <td>0.447</td>\n",
       "      <td>0.959</td>\n",
       "      <td>0.95266</td>\n",
       "      <td>0.0086</td>\n",
       "      <td>1.654000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-+++-</td>\n",
       "      <td>66.8</td>\n",
       "      <td>7</td>\n",
       "      <td>0.003681</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105603</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2319786</td>\n",
       "      <td>64373673</td>\n",
       "      <td>T</td>\n",
       "      <td>G</td>\n",
       "      <td>0.356</td>\n",
       "      <td>0.396</td>\n",
       "      <td>0.955</td>\n",
       "      <td>0.94819</td>\n",
       "      <td>0.0092</td>\n",
       "      <td>8.315000e-09</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>66.5</td>\n",
       "      <td>7</td>\n",
       "      <td>0.003935</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105688</th>\n",
       "      <td>16</td>\n",
       "      <td>rs1074652</td>\n",
       "      <td>64372426</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.358</td>\n",
       "      <td>0.397</td>\n",
       "      <td>0.951</td>\n",
       "      <td>0.94781</td>\n",
       "      <td>0.0092</td>\n",
       "      <td>6.631000e-09</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>64.2</td>\n",
       "      <td>7</td>\n",
       "      <td>0.006597</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>106239</th>\n",
       "      <td>16</td>\n",
       "      <td>rs5817454m</td>\n",
       "      <td>64344770</td>\n",
       "      <td>T</td>\n",
       "      <td>TG</td>\n",
       "      <td>0.671</td>\n",
       "      <td>0.658</td>\n",
       "      <td>0.945</td>\n",
       "      <td>1.05813</td>\n",
       "      <td>0.0100</td>\n",
       "      <td>1.601000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>+???????</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>46945</td>\n",
       "      <td>59700</td>\n",
       "      <td>52551.45</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>106544</th>\n",
       "      <td>16</td>\n",
       "      <td>rs1437146</td>\n",
       "      <td>64346816</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.644</td>\n",
       "      <td>0.604</td>\n",
       "      <td>0.959</td>\n",
       "      <td>1.05401</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>4.425000e-09</td>\n",
       "      <td>1</td>\n",
       "      <td>++-+--++</td>\n",
       "      <td>66.6</td>\n",
       "      <td>7</td>\n",
       "      <td>0.003876</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>108378</th>\n",
       "      <td>16</td>\n",
       "      <td>rs4949071</td>\n",
       "      <td>64333364</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.354</td>\n",
       "      <td>0.393</td>\n",
       "      <td>0.958</td>\n",
       "      <td>0.95047</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>1.556000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>64.7</td>\n",
       "      <td>7</td>\n",
       "      <td>0.005930</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>108524</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2917685</td>\n",
       "      <td>64296852</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.429</td>\n",
       "      <td>0.446</td>\n",
       "      <td>0.957</td>\n",
       "      <td>0.95294</td>\n",
       "      <td>0.0086</td>\n",
       "      <td>2.047000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-+++-</td>\n",
       "      <td>66.8</td>\n",
       "      <td>7</td>\n",
       "      <td>0.003639</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>108633</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2917704</td>\n",
       "      <td>64305723</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0.570</td>\n",
       "      <td>0.554</td>\n",
       "      <td>0.954</td>\n",
       "      <td>1.05001</td>\n",
       "      <td>0.0086</td>\n",
       "      <td>1.402000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>++-+---+</td>\n",
       "      <td>66.9</td>\n",
       "      <td>7</td>\n",
       "      <td>0.003534</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>110181</th>\n",
       "      <td>16</td>\n",
       "      <td>rs2967185</td>\n",
       "      <td>64302814</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.430</td>\n",
       "      <td>0.447</td>\n",
       "      <td>0.960</td>\n",
       "      <td>0.95294</td>\n",
       "      <td>0.0085</td>\n",
       "      <td>1.499000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-+++-</td>\n",
       "      <td>65.7</td>\n",
       "      <td>7</td>\n",
       "      <td>0.004782</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>110426</th>\n",
       "      <td>16</td>\n",
       "      <td>rs9940363</td>\n",
       "      <td>64330132</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.355</td>\n",
       "      <td>0.393</td>\n",
       "      <td>0.957</td>\n",
       "      <td>0.95018</td>\n",
       "      <td>0.0090</td>\n",
       "      <td>1.302000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>--+-++--</td>\n",
       "      <td>64.4</td>\n",
       "      <td>7</td>\n",
       "      <td>0.006345</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>110490</th>\n",
       "      <td>16</td>\n",
       "      <td>rs1583582</td>\n",
       "      <td>64304439</td>\n",
       "      <td>A</td>\n",
       "      <td>C</td>\n",
       "      <td>0.570</td>\n",
       "      <td>0.553</td>\n",
       "      <td>0.957</td>\n",
       "      <td>1.04959</td>\n",
       "      <td>0.0086</td>\n",
       "      <td>1.797000e-08</td>\n",
       "      <td>0</td>\n",
       "      <td>++-+---+</td>\n",
       "      <td>66.8</td>\n",
       "      <td>7</td>\n",
       "      <td>0.003610</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>110788</th>\n",
       "      <td>16</td>\n",
       "      <td>rs34570689</td>\n",
       "      <td>64358287</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>0.666</td>\n",
       "      <td>0.651</td>\n",
       "      <td>0.993</td>\n",
       "      <td>1.05887</td>\n",
       "      <td>0.0096</td>\n",
       "      <td>2.617000e-09</td>\n",
       "      <td>0</td>\n",
       "      <td>++-+????</td>\n",
       "      <td>62.0</td>\n",
       "      <td>3</td>\n",
       "      <td>0.048050</td>\n",
       "      <td>48223</td>\n",
       "      <td>60717</td>\n",
       "      <td>53635.28</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        CHR         SNP         BP A1  A2  FRQ_A_56418  FRQ_U_78818   INFO  \\\n",
       "379       8   rs1434281  103671080  A   G        0.344        0.399  0.957   \n",
       "42353     8   rs4734654  103669991  A   G        0.656        0.601  0.959   \n",
       "99597    16   rs4949087   64333546  A   G        0.354        0.393  0.958   \n",
       "99851    16  rs34707355   64375453  T   C        0.357        0.396  0.954   \n",
       "100535   16   rs9933980   64370514  T   G        0.356        0.396  0.957   \n",
       "101159   16   rs9934855   64326532  T   C        0.646        0.607  0.957   \n",
       "101491   16   rs2917691   64297994  T   C        0.570        0.553  0.959   \n",
       "101607   16   rs2917690   64297917  T   G        0.428        0.445  0.956   \n",
       "101648   16   rs2917695   64299409  C   G        0.584        0.571  0.995   \n",
       "102242   16  rs11643828   64349345  A   T        0.325        0.339  0.994   \n",
       "103280   16  rs12930453   64315466  C   G        0.322        0.335  0.990   \n",
       "103838   16   rs2917701   64302367  A   T        0.584        0.571  0.996   \n",
       "103856   16   rs2319807   64301371  T   C        0.570        0.553  0.959   \n",
       "104002   16   rs2917689   64297905  T   C        0.571        0.554  0.957   \n",
       "104368   16   rs6498941   64329023  T   C        0.355        0.394  0.957   \n",
       "104559   16   rs9935149   64322807  A   C        0.355        0.394  0.956   \n",
       "104977   16   rs4949070   64333189  C   G        0.680        0.666  0.992   \n",
       "105085   16   rs1837017   64298158  T   C        0.430        0.447  0.959   \n",
       "105567   16   rs2967190   64298669  A   G        0.430        0.447  0.959   \n",
       "105603   16   rs2319786   64373673  T   G        0.356        0.396  0.955   \n",
       "105688   16   rs1074652   64372426  T   C        0.358        0.397  0.951   \n",
       "106239   16  rs5817454m   64344770  T  TG        0.671        0.658  0.945   \n",
       "106544   16   rs1437146   64346816  A   G        0.644        0.604  0.959   \n",
       "108378   16   rs4949071   64333364  T   C        0.354        0.393  0.958   \n",
       "108524   16   rs2917685   64296852  T   C        0.429        0.446  0.957   \n",
       "108633   16   rs2917704   64305723  A   G        0.570        0.554  0.954   \n",
       "110181   16   rs2967185   64302814  T   C        0.430        0.447  0.960   \n",
       "110426   16   rs9940363   64330132  T   C        0.355        0.393  0.957   \n",
       "110490   16   rs1583582   64304439  A   C        0.570        0.553  0.957   \n",
       "110788   16  rs34570689   64358287  A   T        0.666        0.651  0.993   \n",
       "\n",
       "             OR      SE             P  ngt Direction  HetISqt  HetDf  \\\n",
       "379     0.94810  0.0095  1.705000e-08    0  -+----+-      0.0      7   \n",
       "42353   1.05443  0.0094  1.503000e-08   24  +-++++-+      0.0      7   \n",
       "99597   0.95037  0.0090  1.372000e-08    0  --+-++--     64.7      7   \n",
       "99851   0.94743  0.0092  5.164000e-09    0  --+-++--     67.4      7   \n",
       "100535  0.94810  0.0090  2.986000e-09    1  --+-++--     65.8      7   \n",
       "101159  1.05243  0.0090  1.285000e-08   15  ++-+--++     63.4      7   \n",
       "101491  1.04970  0.0086  1.634000e-08    0  ++-+---+     66.8      7   \n",
       "101607  0.95266  0.0086  1.713000e-08    0  --+-+++-     65.9      7   \n",
       "101648  1.05232  0.0093  4.129000e-08    0  ++-+????     69.2      3   \n",
       "102242  0.94374  0.0097  2.437000e-09    0  --+-????     63.3      3   \n",
       "103280  0.94554  0.0097  8.075000e-09    0  --+-????     62.6      3   \n",
       "103838  1.05211  0.0092  3.341000e-08   14  ++-+????     67.6      3   \n",
       "103856  1.04938  0.0086  2.025000e-08    0  ++-+---+     66.2      7   \n",
       "104002  1.04949  0.0086  1.845000e-08    0  ++-+---+     65.8      7   \n",
       "104368  0.95009  0.0092  2.928000e-08    1  --+-++--     64.1      7   \n",
       "104559  0.94990  0.0090  1.031000e-08    0  --+-++--     62.5      7   \n",
       "104977  1.05792  0.0098  9.411000e-09    0  ++-+????     65.7      3   \n",
       "105085  0.95256  0.0086  1.571000e-08    0  --+-+++-     66.9      7   \n",
       "105567  0.95266  0.0086  1.654000e-08    0  --+-+++-     66.8      7   \n",
       "105603  0.94819  0.0092  8.315000e-09    0  --+-++--     66.5      7   \n",
       "105688  0.94781  0.0092  6.631000e-09    0  --+-++--     64.2      7   \n",
       "106239  1.05813  0.0100  1.601000e-08    0  +???????      0.0      0   \n",
       "106544  1.05401  0.0090  4.425000e-09    1  ++-+--++     66.6      7   \n",
       "108378  0.95047  0.0090  1.556000e-08    0  --+-++--     64.7      7   \n",
       "108524  0.95294  0.0086  2.047000e-08    0  --+-+++-     66.8      7   \n",
       "108633  1.05001  0.0086  1.402000e-08    0  ++-+---+     66.9      7   \n",
       "110181  0.95294  0.0085  1.499000e-08    0  --+-+++-     65.7      7   \n",
       "110426  0.95018  0.0090  1.302000e-08    0  --+-++--     64.4      7   \n",
       "110490  1.04959  0.0086  1.797000e-08    0  ++-+---+     66.8      7   \n",
       "110788  1.05887  0.0096  2.617000e-09    0  ++-+????     62.0      3   \n",
       "\n",
       "          HetPVa    Nca    Nco      Neff  \n",
       "379     0.573300  56418  78818  64441.44  \n",
       "42353   0.566500  56418  78818  64441.44  \n",
       "99597   0.005922  56418  78818  64441.44  \n",
       "99851   0.003126  56418  78818  64441.44  \n",
       "100535  0.004638  56418  78818  64441.44  \n",
       "101159  0.007763  56418  78818  64441.44  \n",
       "101491  0.003610  56418  78818  64441.44  \n",
       "101607  0.004527  56418  78818  64441.44  \n",
       "101648  0.020900  48223  60717  53635.28  \n",
       "102242  0.042680  48223  60717  53635.28  \n",
       "103280  0.045420  48223  60717  53635.28  \n",
       "103838  0.026080  48223  60717  53635.28  \n",
       "103856  0.004236  56418  78818  64441.44  \n",
       "104002  0.004628  56418  78818  64441.44  \n",
       "104368  0.006824  56418  78818  64441.44  \n",
       "104559  0.009374  56418  78818  64441.44  \n",
       "104977  0.033030  48223  60717  53635.28  \n",
       "105085  0.003515  56418  78818  64441.44  \n",
       "105567  0.003681  56418  78818  64441.44  \n",
       "105603  0.003935  56418  78818  64441.44  \n",
       "105688  0.006597  56418  78818  64441.44  \n",
       "106239  1.000000  46945  59700  52551.45  \n",
       "106544  0.003876  56418  78818  64441.44  \n",
       "108378  0.005930  56418  78818  64441.44  \n",
       "108524  0.003639  56418  78818  64441.44  \n",
       "108633  0.003534  56418  78818  64441.44  \n",
       "110181  0.004782  56418  78818  64441.44  \n",
       "110426  0.006345  56418  78818  64441.44  \n",
       "110490  0.003610  56418  78818  64441.44  \n",
       "110788  0.048050  48223  60717  53635.28  "
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizo_df_filt.head(30)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "trying-awareness",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHR</th>\n",
       "      <th>SNP</th>\n",
       "      <th>BP</th>\n",
       "      <th>A1</th>\n",
       "      <th>A2</th>\n",
       "      <th>FRQ_A_56418</th>\n",
       "      <th>FRQ_U_78818</th>\n",
       "      <th>INFO</th>\n",
       "      <th>OR</th>\n",
       "      <th>SE</th>\n",
       "      <th>P</th>\n",
       "      <th>ngt</th>\n",
       "      <th>Direction</th>\n",
       "      <th>HetISqt</th>\n",
       "      <th>HetDf</th>\n",
       "      <th>HetPVa</th>\n",
       "      <th>Nca</th>\n",
       "      <th>Nco</th>\n",
       "      <th>Neff</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>3061760</th>\n",
       "      <td>7</td>\n",
       "      <td>rs6461049</td>\n",
       "      <td>2017445</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0.542</td>\n",
       "      <td>0.536</td>\n",
       "      <td>0.961</td>\n",
       "      <td>1.07691</td>\n",
       "      <td>0.0088</td>\n",
       "      <td>2.582000e-17</td>\n",
       "      <td>22</td>\n",
       "      <td>++-+++++</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0.6336</td>\n",
       "      <td>56418</td>\n",
       "      <td>78818</td>\n",
       "      <td>64441.44</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "         CHR        SNP       BP A1 A2  FRQ_A_56418  FRQ_U_78818   INFO  \\\n",
       "3061760    7  rs6461049  2017445  T  C        0.542        0.536  0.961   \n",
       "\n",
       "              OR      SE             P  ngt Direction  HetISqt  HetDf  HetPVa  \\\n",
       "3061760  1.07691  0.0088  2.582000e-17   22  ++-+++++      0.0      7  0.6336   \n",
       "\n",
       "           Nca    Nco      Neff  \n",
       "3061760  56418  78818  64441.44  "
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizo_df_filt[schizo_df_filt['SNP']==\"rs6461049\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "dramatic-three",
   "metadata": {},
   "outputs": [],
   "source": [
    "schizo_snps= pd.read_csv(\"schizophrenia_snps.txt\", sep='\\t', names=['SNP'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "tribal-recipient",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>SNP</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>rs6461049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>rs7085104</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>rs1198588</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>rs1006737</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>rs17691888</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>rs4129585</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>rs10789369</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>rs794086</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>rs290542</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>rs2373000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>rs6878284</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>rs4687552</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>rs12991836</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>rs2949006</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>rs4801131</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>rs778371</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>rs14403</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>rs11532322</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>rs1538774</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>rs11995572</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>rs171748</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>rs2910032</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           SNP\n",
       "0    rs6461049\n",
       "1    rs7085104\n",
       "2    rs1198588\n",
       "3    rs1006737\n",
       "4   rs17691888\n",
       "5    rs4129585\n",
       "6   rs10789369\n",
       "7     rs794086\n",
       "8     rs290542\n",
       "9    rs2373000\n",
       "10   rs6878284\n",
       "11   rs4687552\n",
       "12  rs12991836\n",
       "13   rs2949006\n",
       "14   rs4801131\n",
       "15    rs778371\n",
       "16     rs14403\n",
       "17  rs11532322\n",
       "18   rs1538774\n",
       "19  rs11995572\n",
       "20    rs171748\n",
       "21   rs2910032"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "schizo_snps"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "effective-ownership",
   "metadata": {},
   "outputs": [],
   "source": [
    "schizo_df_final= schizo_df_filt.merge(schizo_snps, on=\"SNP\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "id": "bottom-circus",
   "metadata": {},
   "outputs": [],
   "source": [
    "schizo_df_final.sort_values('CHR',ascending=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "tough-canberra",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Process is interrupted.\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "\n",
    "#awk '$2 == \"rs121907970\" {print $2}' 1000Genomes/ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz\n",
    "#bgzip -d /datasets/cs284-sp21-A00-public/1000Genomes/ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -c > ~/teams/CSE284_SP21_A00/team13/chr15.vcf\n",
    "bcftools view --include ID==@ts_snps.list chr15.vcf| cut -f 1-4\n",
    "\n",
    "##/rs387906309//rs147324677//rs76173977//rs138058578//rs121907970/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "alert-somalia",
   "metadata": {},
   "outputs": [],
   "source": [
    "#vcf_df = pd.read_csv(\"1000Genomes/ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz\", sep='\\t', error_bad_lines=False)\n",
    "\n",
    "# import os\n",
    "# filename = \"1000Genomes/ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz\"\n",
    "# lines_number = sum(1 for line in open(filename))\n",
    "# lines_in_chunk = 200\n",
    "# counter = 0\n",
    "# completed = 0\n",
    "# reader = pd.read_csv(filename, chunksize=lines_in_chunk, sep='\\t', error_bad_lines=False )\n",
    "# for chunk in reader:\n",
    "#     # < ... reading the chunk somehow... >\n",
    "#     # showing progress:\n",
    "#     counter += lines_in_chunk\n",
    "#     new_completed = int(round(float(counter)/lines_number * 100))\n",
    "#     if (new_completed > completed): \n",
    "#         completed = new_completed\n",
    "#         print(\"Completed\", completed, \"%\")\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "great-shoulder",
   "metadata": {},
   "outputs": [],
   "source": [
    "chr15_df = pd.read_csv(\"chr15_HG00379_HG00155.txt\", sep='\\t', error_bad_lines=False, skiprows=2, names=['CHROM', 'SNP', 'REF', 'ALT', 'PARENT1', 'PARENT2', 'USELESS', 'CHILD'] )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "royal-bunch",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHROM</th>\n",
       "      <th>SNP</th>\n",
       "      <th>REF</th>\n",
       "      <th>ALT</th>\n",
       "      <th>PARENT1</th>\n",
       "      <th>PARENT2</th>\n",
       "      <th>USELESS</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>20000041</td>\n",
       "      <td>rs371549847</td>\n",
       "      <td>T</td>\n",
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       "      <td>0|0</td>\n",
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       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>20000075</td>\n",
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       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>20000123</td>\n",
       "      <td>rs373298708</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>20000127</td>\n",
       "      <td>rs560310552</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>102520995</td>\n",
       "      <td>rs543980749</td>\n",
       "      <td>CG</td>\n",
       "      <td>C</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>102521010</td>\n",
       "      <td>rs533757656</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>102521041</td>\n",
       "      <td>rs548966424</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>102521057</td>\n",
       "      <td>rs567278523</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>102521131</td>\n",
       "      <td>rs141255594</td>\n",
       "      <td>GGTT</td>\n",
       "      <td>G</td>\n",
       "      <td>0|1</td>\n",
       "      <td>0|1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1|1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2424689 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        CHROM          SNP   REF ALT PARENT1 PARENT2  USELESS CHILD\n",
       "15   20000041  rs371549847     T   A     0|0     0|0      NaN   0|0\n",
       "15   20000075  rs565090028     C   T     0|0     0|0      NaN   0|0\n",
       "15   20000114  rs201219124     G   T     0|0     0|0      NaN   0|0\n",
       "15   20000123  rs373298708     T   C     0|0     0|0      NaN   0|0\n",
       "15   20000127  rs560310552     A   T     0|0     0|0      NaN   0|0\n",
       "..        ...          ...   ...  ..     ...     ...      ...   ...\n",
       "15  102520995  rs543980749    CG   C     0|0     0|0      NaN   0|0\n",
       "15  102521010  rs533757656     G   C     0|0     0|0      NaN   0|0\n",
       "15  102521041  rs548966424     A   G     0|0     0|0      NaN   0|0\n",
       "15  102521057  rs567278523     G   C     0|0     0|0      NaN   0|0\n",
       "15  102521131  rs141255594  GGTT   G     0|1     0|1      NaN   1|1\n",
       "\n",
       "[2424689 rows x 8 columns]"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chr15_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "honey-carrier",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>102520995</td>\n",
       "      <td>rs543980749</td>\n",
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       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>102521041</td>\n",
       "      <td>rs548966424</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
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       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>102521057</td>\n",
       "      <td>rs567278523</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>102521131</td>\n",
       "      <td>rs141255594</td>\n",
       "      <td>GGTT</td>\n",
       "      <td>G</td>\n",
       "      <td>0|1</td>\n",
       "      <td>0|1</td>\n",
       "      <td>1|1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2424689 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        CHROM          SNP   REF ALT PARENT1 PARENT2 CHILD\n",
       "15   20000041  rs371549847     T   A     0|0     0|0   0|0\n",
       "15   20000075  rs565090028     C   T     0|0     0|0   0|0\n",
       "15   20000114  rs201219124     G   T     0|0     0|0   0|0\n",
       "15   20000123  rs373298708     T   C     0|0     0|0   0|0\n",
       "15   20000127  rs560310552     A   T     0|0     0|0   0|0\n",
       "..        ...          ...   ...  ..     ...     ...   ...\n",
       "15  102520995  rs543980749    CG   C     0|0     0|0   0|0\n",
       "15  102521010  rs533757656     G   C     0|0     0|0   0|0\n",
       "15  102521041  rs548966424     A   G     0|0     0|0   0|0\n",
       "15  102521057  rs567278523     G   C     0|0     0|0   0|0\n",
       "15  102521131  rs141255594  GGTT   G     0|1     0|1   1|1\n",
       "\n",
       "[2424689 rows x 7 columns]"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chr15_df = chr15_df.drop('USELESS', axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "id": "superior-choir",
   "metadata": {},
   "outputs": [],
   "source": [
    "ts_snp = chr15_df.loc[chr15_df['SNP']==\"rs76173977\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "id": "sunrise-billion",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHROM</th>\n",
       "      <th>SNP</th>\n",
       "      <th>REF</th>\n",
       "      <th>ALT</th>\n",
       "      <th>PARENT1</th>\n",
       "      <th>PARENT2</th>\n",
       "      <th>USELESS</th>\n",
       "      <th>CHILD</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>72640388</td>\n",
       "      <td>rs76173977</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       CHROM         SNP REF ALT PARENT1 PARENT2  USELESS CHILD\n",
       "15  72640388  rs76173977   C   T     0|0     0|0      NaN   0|0"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ts_snp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "id": "sound-bangkok",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHROM</th>\n",
       "      <th>SNP</th>\n",
       "      <th>REF</th>\n",
       "      <th>ALT</th>\n",
       "      <th>PARENT1</th>\n",
       "      <th>PARENT2</th>\n",
       "      <th>CHILD</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>79050148</td>\n",
       "      <td>rs8079781</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0|1</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       CHROM        SNP REF ALT PARENT1 PARENT2 CHILD\n",
       "17  79050148  rs8079781   C   T     0|1     0|0   0|0"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\n",
    "chr17_df = pd.read_csv(\"chr17_HG00379_HG00155.txt\", sep='\\t', error_bad_lines=False, skiprows=2, names=['CHROM', 'SNP', 'REF', 'ALT', 'PARENT1', 'PARENT2', 'USELESS', 'CHILD'] )\n",
    "chr17_df = chr17_df.drop('USELESS', axis=1)\n",
    "adhd_snp = chr17_df.loc[chr17_df['SNP']==\"rs8079781\"]\n",
    "adhd_snp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "id": "acute-screening",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHROM</th>\n",
       "      <th>SNP</th>\n",
       "      <th>REF</th>\n",
       "      <th>ALT</th>\n",
       "      <th>PARENT1</th>\n",
       "      <th>PARENT2</th>\n",
       "      <th>CHILD</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [CHROM, SNP, REF, ALT, PARENT1, PARENT2, CHILD]\n",
       "Index: []"
      ]
     },
     "execution_count": 54,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chr22_df = pd.read_csv(\"chr22_HG00379_HG00155.txt\", sep='\\t', error_bad_lines=False, skiprows=2, names=['CHROM', 'SNP', 'REF', 'ALT', 'PARENT1', 'PARENT2', 'USELESS', 'CHILD'] )\n",
    "chr22_df = chr22_df.drop('USELESS', axis=1)\n",
    "neuro_snp = chr22_df.loc[chr22_df['SNP']==\"rs189150283\"]\n",
    "neuro_snp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "id": "false-overhead",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "\n",
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CHROM</th>\n",
       "      <th>SNP</th>\n",
       "      <th>REF</th>\n",
       "      <th>ALT</th>\n",
       "      <th>PARENT1</th>\n",
       "      <th>PARENT2</th>\n",
       "      <th>CHILD</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>44440146</td>\n",
       "      <td>rs4660761</td>\n",
       "      <td>G</td>\n",
       "      <td>A</td>\n",
       "      <td>0|1</td>\n",
       "      <td>1|1</td>\n",
       "      <td>0|1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      CHROM        SNP REF ALT PARENT1 PARENT2 CHILD\n",
       "1  44440146  rs4660761   G   A     0|1     1|1   0|1"
      ]
     },
     "execution_count": 55,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chr1_df = pd.read_csv(\"chr1_HG00379_HG00155.txt\", sep='\\t', error_bad_lines=False, skiprows=2, names=['CHROM', 'SNP', 'REF', 'ALT', 'PARENT1', 'PARENT2', 'USELESS', 'CHILD'] )\n",
    "chr1_df = chr1_df.drop('USELESS', axis=1)\n",
    "neuro_snp = chr1_df.loc[chr1_df['SNP']==\"rs4660761\"]\n",
    "neuro_snp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "id": "collective-illustration",
   "metadata": {},
   "outputs": [],
   "source": [
    "chr15_df = pd.read_csv(\"chr15_HG00379_HG00155.txt\", sep='\\t', error_bad_lines=False, skiprows=2, names=['CHROM','BP', 'SNP', 'REF', 'ALT', 'PARENT1', 'PARENT2', 'USELESS', 'CHILD','EXTRA'], index_col=False )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "id": "unknown-expansion",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
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       "      <td>T</td>\n",
       "      <td>A</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>15</td>\n",
       "      <td>20000075</td>\n",
       "      <td>rs565090028</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>15</td>\n",
       "      <td>20000114</td>\n",
       "      <td>rs201219124</td>\n",
       "      <td>G</td>\n",
       "      <td>T</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>15</td>\n",
       "      <td>20000123</td>\n",
       "      <td>rs373298708</td>\n",
       "      <td>T</td>\n",
       "      <td>C</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>15</td>\n",
       "      <td>20000127</td>\n",
       "      <td>rs560310552</td>\n",
       "      <td>A</td>\n",
       "      <td>T</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2424684</th>\n",
       "      <td>15</td>\n",
       "      <td>102520995</td>\n",
       "      <td>rs543980749</td>\n",
       "      <td>CG</td>\n",
       "      <td>C</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2424685</th>\n",
       "      <td>15</td>\n",
       "      <td>102521010</td>\n",
       "      <td>rs533757656</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2424686</th>\n",
       "      <td>15</td>\n",
       "      <td>102521041</td>\n",
       "      <td>rs548966424</td>\n",
       "      <td>A</td>\n",
       "      <td>G</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2424687</th>\n",
       "      <td>15</td>\n",
       "      <td>102521057</td>\n",
       "      <td>rs567278523</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>0|0</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0|0</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2424688</th>\n",
       "      <td>15</td>\n",
       "      <td>102521131</td>\n",
       "      <td>rs141255594</td>\n",
       "      <td>GGTT</td>\n",
       "      <td>G</td>\n",
       "      <td>0|1</td>\n",
       "      <td>0|1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1|1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2424689 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         CHROM         BP          SNP   REF ALT PARENT1 PARENT2  USELESS  \\\n",
       "0           15   20000041  rs371549847     T   A     0|0     0|0      NaN   \n",
       "1           15   20000075  rs565090028     C   T     0|0     0|0      NaN   \n",
       "2           15   20000114  rs201219124     G   T     0|0     0|0      NaN   \n",
       "3           15   20000123  rs373298708     T   C     0|0     0|0      NaN   \n",
       "4           15   20000127  rs560310552     A   T     0|0     0|0      NaN   \n",
       "...        ...        ...          ...   ...  ..     ...     ...      ...   \n",
       "2424684     15  102520995  rs543980749    CG   C     0|0     0|0      NaN   \n",
       "2424685     15  102521010  rs533757656     G   C     0|0     0|0      NaN   \n",
       "2424686     15  102521041  rs548966424     A   G     0|0     0|0      NaN   \n",
       "2424687     15  102521057  rs567278523     G   C     0|0     0|0      NaN   \n",
       "2424688     15  102521131  rs141255594  GGTT   G     0|1     0|1      NaN   \n",
       "\n",
       "        CHILD  EXTRA  \n",
       "0         0|0    NaN  \n",
       "1         0|0    NaN  \n",
       "2         0|0    NaN  \n",
       "3         0|0    NaN  \n",
       "4         0|0    NaN  \n",
       "...       ...    ...  \n",
       "2424684   0|0    NaN  \n",
       "2424685   0|0    NaN  \n",
       "2424686   0|0    NaN  \n",
       "2424687   0|0    NaN  \n",
       "2424688   1|1    NaN  \n",
       "\n",
       "[2424689 rows x 10 columns]"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chr15_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "purple-percentage",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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