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indels (#26)
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Flag sequences with suspected indels based on lengths of known and previously observed alleles.
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@rnmitchell
rnmitchell authored Jun 15, 2020
1 parent 9ac308e commit bf7e4b4
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Showing 4 changed files with 1,201 additions and 1,122 deletions.
2 changes: 1 addition & 1 deletion lusSTR/annot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ def main(args):
if not args.uas and args.kit == 'forenseq':
flank_summary = [
sampleid, project, analysis, locus, reads, marker.canonical, marker.sequence,
marker.flank_5p, marker.annotation, marker.flank_3p, "NA"
marker.flank_5p, marker.annotation, marker.flank_3p, marker.indel_flag
]
flanks_list.append(flank_summary)

Expand Down
125 changes: 98 additions & 27 deletions lusSTR/str_markers.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,8 @@
"Foren_5": 6,
"Foren_3": 14,
"Power_5": 13,
"Power_3": 107
"Power_3": 107,
"Alleles": ["6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16"]
},
"D10S1248": {
"BasesToSubtract": 0,
Expand All @@ -29,7 +30,10 @@
"Foren_5": 18,
"Foren_3": 23,
"Power_5": 57,
"Power_3": 1
"Power_3": 1,
"Alleles": [
"7", "8", "9", "10", "11", "12", "12.3", "13", "14", "15", "16", "17", "18", "19"
]
},
"D12S391": {
"BasesToSubtract": 0,
Expand All @@ -46,7 +50,12 @@
"Foren_5": 39,
"Foren_3": 73,
"Power_5": 21,
"Power_3": 11
"Power_3": 11,
"Alleles": [
"13", "14", "15", "15.1", "16", "16.3", "17", "17.1", "17.3", "18", "18.1",
"18.3", "19", "19.1", "19.2", "19.3", "20", "20.1", "20.3", "21", "21.1", "22",
"22.2", "23", "24", "24.3", "25", "26", "27", "28"
]

},
"D13S317": {
Expand All @@ -67,7 +76,8 @@
"Foren_5": 39,
"Foren_3": 8,
"Power_5": 70,
"Power_3": 43
"Power_3": 43,
"Alleles": ["6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "28.2"]
},
"D16S539": {
"BasesToSubtract": 0,
Expand All @@ -83,7 +93,8 @@
"Foren_5": 38,
"Foren_3": 36,
"Power_5": 133,
"Power_3": 4
"Power_3": 4,
"Alleles": ["5", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16"]
},
"D17S1301": {
"BasesToSubtract": 0,
Expand All @@ -97,7 +108,8 @@
"Sec": "",
"Tert": "",
"Foren_5": 9,
"Foren_3": 16
"Foren_3": 16,
"Alleles": ["7", "8", "9", "10", "11", "11.3", "12", "13", "14", "15"]
},
"D18S51": {
"BasesToSubtract": 10,
Expand All @@ -115,7 +127,12 @@
"Foren_5": 5,
"Foren_3": 48,
"Power_5": 64,
"Power_3": 43
"Power_3": 43,
"Alleles": [
"9", "10", "11", "12", "12.2", "13", "13.2", "14", "14.2", "15", "15.2", "16",
"16.2", "17", "17.2", "18", "18.1", "18.2", "19", "20", "20.2", "21", "21.2", "22",
"23", "24", "25", "28"
]
},
"D19S433": {
"BasesToSubtract": 26,
Expand All @@ -133,7 +150,11 @@
"Foren_5": 12,
"Foren_3": 54,
"Power_5": 61,
"Power_3": 39
"Power_3": 39,
"Alleles": [
"4", "8", "9", "10", "11", "11.2", "12", "12.1", "12.2", "12.3", "13", "13.2",
"14", "14.2", "15", "15.2", "15.3", "16", "16.2", "17", "17.2", "18", "18.2"
]
},
"D1S1656": {
"BasesToSubtract": 10,
Expand All @@ -153,7 +174,11 @@
"Foren_5": 51,
"Foren_3": 0,
"Power_5": 46,
"Power_3": 21
"Power_3": 21,
"Alleles": [
"7", "8", "9", "10", "11", "12", "13", "14", "14.3", "15", "15.3", "16", "16.1",
"16.3", "17", "17.3", "18", "18.3", "19.3", "20"
]
},
"D20S482": {
"BasesToSubtract": 0,
Expand All @@ -167,7 +192,8 @@
"Sec": "",
"Tert": "",
"Foren_5": 18,
"Foren_3": 24
"Foren_3": 24,
"Alleles": ["9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19"]
},
"D21S11": {
"BasesToSubtract": 11,
Expand All @@ -184,7 +210,12 @@
"Foren_5": 34,
"Foren_3": 12,
"Power_5": 10,
"Power_3": 41
"Power_3": 41,
"Alleles": [
"24.2", "25.2", "26", "26.2", "27", "28", "28.2", "28.3", "29", "29.2", "29.3",
"30", "30.2", "30.3", "31", "31.2", "32", "32.2", "33", "33.1", "33.2", "34",
"34.2", "35", "35.2", "36", "37", "38", "39"
]
},
"D22S1045": {
"BasesToSubtract": 0,
Expand All @@ -200,7 +231,8 @@
"Foren_5": 106,
"Foren_3": 20,
"Power_5": 52,
"Power_3": 11
"Power_3": 11,
"Alleles": ["8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19"]
},
"D2S1338": {
"BasesToSubtract": 0,
Expand All @@ -217,7 +249,11 @@
"Foren_5": 3,
"Foren_3": 14,
"Power_5": 66,
"Power_3": 46
"Power_3": 46,
"Alleles": [
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27",
"28"
]
},
"D2S441": {
"BasesToSubtract": 0,
Expand All @@ -234,7 +270,11 @@
"Foren_5": 29,
"Foren_3": 23,
"Power_5": 83,
"Power_3": 4
"Power_3": 4,
"Alleles": [
"9", "10", "10.3", "11", "11.3", "12", "12.3", "13", "14", "15", "16", "17", "18",
"19", "20", "21", "22", "23", "24", "25", "26", "27", "28"
]
},
"D3S1358": {
"BasesToSubtract": 0,
Expand All @@ -251,7 +291,11 @@
"Foren_5": 48,
"Foren_3": 18,
"Power_5": 97,
"Power_3": 18
"Power_3": 18,
"Alleles": [
"10", "11", "12", "13", "14", "15", "15.2", "16", "16.2", "17", "18", "18.2",
"19", "20"
]
},
"D4S2408": {
"BasesToSubtract": 0,
Expand All @@ -265,7 +309,8 @@
"Sec": "CTCT",
"Tert": "",
"Foren_5": 6,
"Foren_3": 8
"Foren_3": 8,
"Alleles": ["7", "8", "9", "10", "11", "12", "13"]
},
"D5S818": {
"BasesToSubtract": 4,
Expand All @@ -281,7 +326,8 @@
"Foren_5": 9,
"Foren_3": 7,
"Power_5": 36,
"Power_3": 82
"Power_3": 82,
"Alleles": ["7", "8", "9", "10", "11", "11.1", "12", "13", "14", "15", "16"]
},
"D6S1043": {
"BasesToSubtract": 0,
Expand All @@ -296,7 +342,11 @@
"Sec": "ATGT",
"Tert": "",
"Foren_5": 65,
"Foren_3": 20
"Foren_3": 20,
"Alleles": [
"8", "9", "10", "11", "12", "12.3", "13", "14", "15", "16", "17", "18", "18.1",
"18.2", "18.3", "19", "19.3", "20", "20.3", "21", "21.3", "22", "22.3", "23", "23.3", "24", "25", "26"
]
},
"D7S820": {
"BasesToSubtract": 16,
Expand All @@ -313,7 +363,11 @@
"Foren_5": 19,
"Foren_3": 20,
"Power_5": 63,
"Power_3": 67
"Power_3": 67,
"Alleles": [
"6", "6.3", "7", "8", "8.1", "9", "9.1", "9.2", "10", "10.1", "10.3", "11", "11.1",
"12", "12.1", "13", "14"
]
},
"D8S1179": {
"BasesToSubtract": 0,
Expand All @@ -330,7 +384,8 @@
"Foren_5": 0,
"Foren_3": 5,
"Power_5": 19,
"Power_3": 108
"Power_3": 108,
"Alleles": ["8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18"]
},
"D9S1122": {
"BasesToSubtract": 0,
Expand All @@ -345,7 +400,8 @@
"Sec": "",
"Tert": "",
"Foren_5": 17,
"Foren_3": 7
"Foren_3": 7,
"Alleles": ["7", "9", "10", "11", "12", "13", "14", "15", "16", "17"]
},
"FGA": {
"BasesToSubtract": 0,
Expand All @@ -365,7 +421,11 @@
"Foren_5": 23,
"Foren_3": 0,
"Power_5": 81,
"Power_3": 0
"Power_3": 0,
"Alleles": [
"17", "18", "19", "19.2", "20", "21", "22", "22.2", "23", "23.2", "24", "25",
"26", "26.2", "27"
]
},
"PentaD": {
"BasesToSubtract": 5,
Expand All @@ -381,7 +441,11 @@
"Foren_5": 100,
"Foren_3": 9,
"Power_5": 62,
"Power_3": 63
"Power_3": 63,
"Alleles": [
"1.2", "2.2", "3.2", "5", "6", "7", "8", "9", "10", "11", "12", "13", "13.4",
"14", "14.1", "15", "16", "17"
]
},
"PentaE": {
"BasesToSubtract": 0,
Expand All @@ -397,7 +461,11 @@
"Foren_5": 19,
"Foren_3": 75,
"Power_5": 108,
"Power_3": 0
"Power_3": 0,
"Alleles": [
"5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "15.4", "16", "16.4",
"17", "18", "19", "19.4", "20", "21", "22", "23", "24", "25"
]
},
"TH01": {
"BasesToSubtract": 0,
Expand All @@ -413,7 +481,8 @@
"Foren_5": 32,
"Foren_3": 12,
"Power_5": 7,
"Power_3": 156
"Power_3": 156,
"Alleles": ["5", "6", "7", "7.3", "8", "8.3", "9", "9.3", "10", "10.3", "11"]
},
"TPOX": {
"BasesToSubtract": 0,
Expand All @@ -429,7 +498,8 @@
"Foren_5": 2,
"Foren_3": 5,
"Power_5": 121,
"Power_3": 14
"Power_3": 14,
"Alleles": ["5", "6", "7", "8", "9", "10", "11", "12", "13", "14"]
},
"vWA": {
"BasesToSubtract": 8,
Expand All @@ -447,6 +517,7 @@
"Foren_5": 19,
"Foren_3": 5,
"Power_5": 4,
"Power_3": 100
"Power_3": 100,
"Alleles": ["11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21"]
}
}
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