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ProgramOptions.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<title>Untitled Document</title>
<style type="text/css">
<!--
.style1 {
color: #FF0000;
font-weight: bold;
}
-->
</style>
</head>
<body>
<table border="1" cellspacing="0" cellpadding="0" width="583">
<tr>
<td width="583" colspan="9" valign="top"><p><strong><u>PE_BASH_MAKER.py</u></strong></p></td>
</tr>
<tr>
<td width="67" valign="top"><p><em>Usage: </em></p></td>
<td width="516" colspan="8" valign="top"><p>PE_BASH_MAKER.py --ref REF --r1src R1SRC.fq --r2src R2SRC.fq<br />
--min MINMEM --max MAXMEM --cut CUTOFF --Ncut NCUT <br />
--rlength RLENGTH --blength BLENGTH --slength SLENGTH <br />
--read_type READ_TYPE --filt FILT [--progInd PROGIND] [--isize ISIZE] [--absolute] [--parallel]</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Required arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--ref</p></td>
<td width="390" colspan="7" valign="top"><p>The reference genome.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--r1src, <br />
--r2src</p></td>
<td width="390" colspan="7" valign="top"><p>Input fastq files containing the raw sequence data. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--min, --max</p></td>
<td width="390" colspan="7" valign="top"><p>Equivalent to --minmem, --maxmem used in ConsensusMaker.py, see below. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--blength</p></td>
<td width="390" colspan="7" valign="top"><p>Equivalent to --barcode_length used in tag_to_header.py, see below. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--slength</p></td>
<td width="390" colspan="7" valign="top"><p>Equivalent to --spacer_length used in tag_to_header.py, see below. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--rlength</p></td>
<td width="390" colspan="7" valign="top"><p>Length of the original untrimmed read [101]. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--cut, --Ncut,<br />
--read_type, --filt</p></td>
<td width="390" colspan="7" valign="top"><p>Equivalent to the options of the same name in ConsensusMaker.py, see below. </p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Optional arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-h</p></td>
<td width="390" colspan="7" valign="top"><p>Show a help message and exit. Useful for entering commands because it shows all the arguments. Should only be entered by itself. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--progInd</p></td>
<td width="390" colspan="7" valign="top"><p>Equivalent to --read_out in tag_to+header.py, see below. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--isize</p></td>
<td width="390" colspan="7" valign="top"><p>Equivalent to the command of the same name in ConsensusMaker.py, see below.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--absolute</p></td>
<td width="390" colspan="7" valign="top"><p>The location entered for the program when running is an absolute position, not a relative position.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--parallel</p></td>
<td width="390" colspan="7" valign="top"><p>Run alignments in parallel. Not currently supported. </p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><strong><u> </u></strong></p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><strong><u>tag_to_header.py</u></strong></p></td>
</tr>
<tr>
<td width="67" valign="top"><p><em>Usage: </em></p></td>
<td width="516" colspan="8" valign="top"><p>tag_to_header.py --infile1 INFILE1.fq --infile2 INFILE2.fq --outfile1 OUTFILE1.fq.smi --outfile2 OUTFILE2.fq.smi --barcode_length BLENGTH --spacer_length SLENGTH [--read_out ROUT] [--adapter ADAPTERSEQ]</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Required arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--infile1, <br />
--infile2</p></td>
<td width="390" colspan="7" valign="top"><p>Inp<a name="_GoBack" id="_GoBack"></a>ut fastq files containing the raw sequence data. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--outfile1, <br />
--outfile2</p></td>
<td width="390" colspan="7" valign="top"><p>Output fastq files for post-tag_to_header sequences.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--barcode_length</p></td>
<td width="390" colspan="7" valign="top"><p>Length of the duplex tag sequence. [12]</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--spacer_length</p></td>
<td width="390" colspan="7" valign="top"><p>Length of the spacer sequences used. [5]</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Optional arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-h</p></td>
<td width="390" colspan="7" valign="top"><p>Show a help message and exit. Useful for entering commands because it shows all the arguments. Should only be entered by itself. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--adapter</p></td>
<td width="390" colspan="7" valign="top"><p>Optional: Spacer sequence for filtering on the presence of the spacer. This could be thrown off by low quality scores.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--read_out</p></td>
<td width="390" colspan="7" valign="top"><p>How often you want to be told what the program is doing. Defaults to 1000000. In most cases, this is higher than the number of SSCS reads. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="236" colspan="5" valign="top"><p> </p></td>
<td width="38" valign="top"><p> </p></td>
<td width="116" valign="top"><p> </p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><strong><u>ConsensusMaker.py</u></strong></p></td>
</tr>
<tr>
<td width="67" valign="top"><p><em>Usage: </em></p></td>
<td width="516" colspan="8" valign="top"><p>ConsensusMaker.py --infile INFILE --tagfile TAGFILE --outfile OUTFILE --minmem MINMEM --maxmem MAXMEM --cutoff CUTOFF --Ncutoff NCUTOFF --readlength READ_LENGTH --read_type READ_TYPE --filt FILT [--isize ISIZE] [--read_out ROUT] [--rep_filt REP_FILT]</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Required arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--infile </p></td>
<td width="390" colspan="7" valign="top"><p>Sorted, paired-end .bam file containing aligned sequences. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--outfile</p></td>
<td width="390" colspan="7" valign="top"><p>Output bam file for SSCSs. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--tagfile </p></td>
<td width="390" colspan="7" valign="top"><p>output tagcounts file</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--minmem</p></td>
<td width="390" colspan="7" valign="top"><p>Minimum number of reads allowed to comprise a consensus. [3]</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--maxmem</p></td>
<td width="390" colspan="7" valign="top"><p>Maximum number of reads allowed to comprise a consensus. [1000]</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="390" colspan="7" valign="top"><p>--minmem and --maxmem set the range of family sizes (constrained by cigar string) that can be used to make a consensus sequence. Examples use --minmem of 3 and --maxmem of 1000</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p>Example 1: </p></td>
<td width="264" colspan="3" valign="top"><p>Ten reads (readlength = 80) have a particular barcode. Of these ten, nine of them have a cigar string of 80M, while one has a cigar string of 39M1I40M. Only the nine with a cigar string of 80M are sent on to be made into a SSCS.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p>Example 2:</p></td>
<td width="264" colspan="3" valign="top"><p>Three reads (readlength 80) have a particular barcode. Of these, two have a cigar string of 80M, and one has a cigar string of 20M1D60M. No SSCS results.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p>Example 3: </p></td>
<td width="264" colspan="3" valign="top"><p>A family with over 1000 members exists. A random sample of 1000 reads from that family is used to make a SSCS.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--cutoff</p></td>
<td width="390" colspan="7" valign="top"><p>Percentage of nucleotides at a given position in a read that must be identical in order for a consensus be called at that position. [0.7] </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p>Example:<br />
--cutoff = 0.7</p></td>
<td width="264" colspan="3" valign="top"><p>Four reads (readlength = 10) are as follows:</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p> </p></td>
<td width="264" colspan="3" valign="top"><p>Read 1: ACTGATACTT</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p> </p></td>
<td width="264" colspan="3" valign="top"><p>Read 2: ACTGAAACCT</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p> </p></td>
<td width="264" colspan="3" valign="top"><p>Read 3: ACTGATACCT</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p> </p></td>
<td width="264" colspan="3" valign="top"><p>Read 4: ACTGATACTT</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p> </p></td>
<td width="264" colspan="3" valign="top"><p>The resulting SSCS is:</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p> </p></td>
<td width="264" colspan="3" valign="top"><p> ACTGATACNT</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--Ncutoff</p></td>
<td width="390" colspan="7" valign="top"><p>With --filt 'n', maximum fraction of Ns allowed in a consensus [1.0]</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p>Example:<br />
--Ncutoff = .1, <br />
--readlength = 20</p></td>
<td width="264" colspan="3" valign="top"><p>Two SSCSs are generated as follows:</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="66" colspan="2" valign="top"><p> </p></td>
<td width="324" colspan="5" valign="top"><p>SSCS 1: ACGTGANCTAGTNCTNTACC</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="66" colspan="2" valign="top"><p> </p></td>
<td width="324" colspan="5" valign="top"><p>SSCS 2: GATCTAGTNCATGACCGATA</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="66" colspan="2" valign="top"><p> </p></td>
<td width="324" colspan="5" valign="top"><p>SSCS 2 passes the N filter (10%) with 1/20 = 5% Ns, while SSCS 1 does not with 3/20 = 15% Ns.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--readlength </p></td>
<td width="390" colspan="7" valign="top"><p>Length of the input read that is being used. [80]<br />
If this value is set incorrectly, the program will often crash with an error message about sequence length not matching quality score length, or will output an empty SSCS bam file. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--read_type</p></td>
<td width="390" colspan="7" valign="top"><p>A string specifying which types of read to consider. ['dpm']</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="236" colspan="5" valign="top"><p>Options are:</p></td>
<td width="38" valign="top"><p> </p></td>
<td width="116" valign="top"><p> </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="54" valign="top"><p> </p></td>
<td width="336" colspan="6" valign="top"><p>d: Paired-end reads where both reads in the pair map, and where the two are properly paired (read 2 maps in the opposite direction and on the opposite strand from read 1). </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="72" colspan="3" valign="top"><p> </p></td>
<td width="318" colspan="4" valign="top"><p>Flags are 99, 83, 163, and 147.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="54" valign="top"><p> </p></td>
<td width="336" colspan="6" valign="top"><p>p: Paired-end reads where both reads in the pair map, but the two are not properly paired. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="72" colspan="3" valign="top"><p> </p></td>
<td width="318" colspan="4" valign="top"><p>Flags are 97, 81, 161, 145, 129, 65, 177, and 113.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="54" valign="top"><p> </p></td>
<td width="336" colspan="6" valign="top"><p>m: Paired-end reads where only one read in the pair maps. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="72" colspan="3" valign="top"><p> </p></td>
<td width="318" colspan="4" valign="top"><p>Flags are 181, 117, 137, 133, 73, 89, 69, and 153.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="54" valign="top"><p> </p></td>
<td width="336" colspan="6" valign="top"><p>n: Paired-end reads where neither read in the pair maps, and single end unmapped reads. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="72" colspan="3" valign="top"><p> </p></td>
<td width="318" colspan="4" valign="top"><p>Flags are 141, 77, and 4. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="54" valign="top"><p> </p></td>
<td width="336" colspan="6" valign="top"><p>s: Single end mapped reads. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="72" colspan="3" valign="top"><p> </p></td>
<td width="318" colspan="4" valign="top"><p>Flags are 0 and 16. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--filt </p></td>
<td width="390" colspan="7" valign="top"><p>A string indicating which filters should be implemented. ['os']’</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="236" colspan="5" valign="top"><p>Filters are:</p></td>
<td width="38" valign="top"><p> </p></td>
<td width="116" valign="top"><p> </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="54" valign="top"><p> </p></td>
<td width="336" colspan="6" valign="top"><p>o: Overlap filter. Filters out any read pairs which overlap. Only works on reads of type d (see above).</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="54" valign="top"><p> </p></td>
<td width="336" colspan="6" valign="top"><p>s: Softclipping filter. Filters out any reads which have been soft- clipped in alignment. This avoids later problems.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="54" valign="top"><p> </p></td>
<td width="336" colspan="6" valign="top"><p>n: N filter. Filters out consensus sequences with a higher percentage of Ns than the threshold imposed by --Ncutoff. Without this option, <br />
--Ncutoff doesn't do anything. </p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Optional arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-h</p></td>
<td width="390" colspan="7" valign="top"><p>Show a help message and exit. Useful for entering commands because it shows all the arguments. Should only be entered by itself. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--isize </p></td>
<td width="390" colspan="7" valign="top"><p>If not -1, sets the maximum distance between read 1 and read 2 for the two to not be considered unpaired. Only works if --read_type is 'd' [-1].</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--rep_filt </p></td>
<td width="390" colspan="7" valign="top"><p>Remove tags with homomeric runs of nucleotides of length x. [9]</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--read_out</p></td>
<td width="390" colspan="7" valign="top"><p>How often you want to be told what the program is doing. Defaults to 1000000. In most cases, this is higher than the number of SSCS reads. </p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><strong><u>DuplexMaker.py</u></strong></p></td>
</tr>
<tr>
<td width="67" valign="top"><p><em>Usage: </em></p></td>
<td width="516" colspan="8" valign="top"><p>DuplexMaker.py --infile INFILE --outfile OUTFILE --Ncutoff NCUTOFF --readlength READ_LENGTH --barcode_length BLENGTH [--read_out ROUT]</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Required arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--infile</p></td>
<td width="390" colspan="7" valign="top"><p>Input .bam file containing sorted SSCSs. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--outfile </p></td>
<td width="390" colspan="7" valign="top"><p>Output .bam file.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--Ncutoff</p></td>
<td width="390" colspan="7" valign="top"><p> Maximum percentage of Ns allowed in a consensus [1.0]</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="126" colspan="4" valign="top"><p>Example:<br />
--Ncutoff = .1<br />
--readlength = 20</p></td>
<td width="264" colspan="3" valign="top"><p>Two DCSs are generated as follows:</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="72" colspan="3" valign="top"><p> </p></td>
<td width="318" colspan="4" valign="top"><p>DCS 1: ACGTGANCTAGTNCTNTACC</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="72" colspan="3" valign="top"><p> </p></td>
<td width="318" colspan="4" valign="top"><p>DCS 2: GATCTAGTNCATGACCGATA</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="72" colspan="3" valign="top"><p> </p></td>
<td width="318" colspan="4" valign="top"><p>DCS 2 passes the n filter (10%) with 1/20 = 5% Ns, while DCS 1 does not with 3/20 = 15% Ns.</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--readlength</p></td>
<td width="390" colspan="7" valign="top"><p>Length of the input read that is being used. [80]<br />
If this value is set incorrectly, the program will often crash with an error message about sequence length not matching quality score length, or will output an empty DCS bam file. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--barcode_length</p></td>
<td width="390" colspan="7" valign="top"><p>Length of the barcode sequence. Should match the value in tag_to_header. [12]</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Optional Arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-h</p></td>
<td width="390" colspan="7" valign="top"><p>Show a help message and exit. Useful for entering commands because it shows all the arguments. Should only be entered by itself. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>--read_out</p></td>
<td width="390" colspan="7" valign="top"><p>How often you want to be told what the program is doing. Defaults to 1000000. In most cases, this is higher than the number of SSCS reads. </p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><strong><u>CountMuts.py</u></strong></p></td>
</tr>
<tr>
<td width="67" valign="top"><p><em>Usage: </em></p></td>
<td width="516" colspan="8" valign="top"><p>Cat INFILE.pileup | CountMuts.py d MINDEPTH -C MAX_CLONALITY <br />
-c MIN_CLONALITY -n N_CUTOFF [-s START] [-e END] [-u]</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Required arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-d</p></td>
<td width="390" colspan="7" valign="top"><p>Minimum depth for counting mutations at a site <br />
(default = 20).</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-C</p></td>
<td width="390" colspan="7" valign="top"><p>Upper cutoff of mutant reads for scoring a clonal mutation (default = 0.1).</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-c</p></td>
<td width="390" colspan="7" valign="top"><p>Lower cutoff of mutant reads for scoring a clonal mutation (default = 0).</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-n</p></td>
<td width="390" colspan="7" valign="top"><p>Maximum fraction of N's allowed to score a position (default = 0.05).</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Optional Arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-h</p></td>
<td width="390" colspan="7" valign="top"><p>Show a help message and exit. Useful for entering commands because it shows all the arguments. Should only be entered by itself. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-s</p></td>
<td width="390" colspan="7" valign="top"><p>Position at which to start scoring for mutations<br />
(default = 0). </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-e</p></td>
<td width="390" colspan="7" valign="top"><p>Position at which to stop scoring for mutations. If set to 0, no position filtering will be performed (default = 0).</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-u</p></td>
<td width="390" colspan="7" valign="top"><p>Only count one mutation of a given type per position</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="390" colspan="7" valign="top"><p> </p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><strong><u>mut-position.py</u></strong></p></td>
</tr>
<tr>
<td width="67" valign="top"><p><em>Usage: </em></p></td>
<td width="516" colspan="8" valign="top"><p>mut-position.py -i INFILE -o OUTFILE -d MINDEPTH<br />
-c CLONAL_MIN -C CLONAL_MAX -n NUM_MUTS</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Required arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-i</p></td>
<td width="390" colspan="7" valign="top"><p>An imput file. If None, defaults to stdin [None].</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-o</p></td>
<td width="390" colspan="7" valign="top"><p>A filename for the output file. If None, outputs to stdout [None]. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-d</p></td>
<td width="390" colspan="7" valign="top"><p>Minimum depth for counting mutations at a site <br />
(default = 20).</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-C</p></td>
<td width="390" colspan="7" valign="top"><p>Upper cutoff of mutant reads for scoring a clonal mutation (default = 0.1).</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-c</p></td>
<td width="390" colspan="7" valign="top"><p>Lower cutoff of mutant reads for scoring a clonal mutation (default = 0).</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-n</p></td>
<td width="390" colspan="7" valign="top"><p>Minimum number of mutations for scoring a site [0]</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Optional Arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-h</p></td>
<td width="390" colspan="7" valign="top"><p>Show a help message and exit. Useful for entering commands because it shows all the arguments. Should only be entered by itself. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="390" colspan="7" valign="top"><p> </p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><strong><u>muts_by_read_position.py</u></strong></p></td>
</tr>
<tr>
<td width="67" valign="top"><p><em>Usage: </em></p></td>
<td width="516" colspan="8" valign="top"><p>muts_by_read_position.py -i INFILE -o OUTFILE -l RLENGTH -C MAX_CLONALITY</p></td>
</tr>
<tr>
<td width="67" valign="top"><p><em> </em></p></td>
<td width="516" colspan="8" valign="top"><p class="style1">NOTE: This program is still under development and is not supported. It can still be used to gain a general idea of bias in N generation and mutations throughout a read, but values may be a bit off. </p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Required arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-i</p></td>
<td width="390" colspan="7" valign="top"><p>An imput file. If None, defaults to stdin [None].</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-o</p></td>
<td width="390" colspan="7" valign="top"><p>A filename for the output file. If None, outputs to generates one from the input file name. Required if -i is not used [None]. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-l</p></td>
<td width="390" colspan="7" valign="top"><p>The length of a single read</p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-C</p></td>
<td width="390" colspan="7" valign="top"><p>Maximum clonality to allow when considering a position [0.1]. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-n</p></td>
<td width="390" colspan="7" valign="top"><p>Maximum fraction of N's allowed to score a position (default = 0.05).</p></td>
</tr>
<tr>
<td width="583" colspan="9" valign="top"><p><em>Optional Arguments:</em></p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p>-h</p></td>
<td width="390" colspan="7" valign="top"><p>Show a help message and exit. Useful for entering commands because it shows all the arguments. Should only be entered by itself. </p></td>
</tr>
<tr>
<td width="67" valign="top"><p> </p></td>
<td width="126" valign="top"><p> </p></td>
<td width="390" colspan="7" valign="top"><p> </p></td>
</tr>
</table>
<p> </p>
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