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140 lines
7.8 KiB
XML
140 lines
7.8 KiB
XML
<tool id="indel_sam2interval" name="Extract indels" version="1.0.0">
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<description>from SAM</description>
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<command interpreter="python">
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indel_sam2interval.py
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--input=$input1
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--include_base=$include_base
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--collapse=$collapse
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--int_out=$output1
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#if $ins_out.include_ins_out == "true"
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--bed_ins_out=$output2
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#else
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--bed_ins_out="None"
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#end if
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#if $del_out.include_del_out == "true"
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--bed_del_out=$output3
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#else
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--bed_del_out="None"
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#end if
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</command>
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<inputs>
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<param format="sam" name="input1" type="data" label="Select dataset to convert" />
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<param name="include_base" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Include the relevant base(s) for each insertion (and a dash (-) for deletions)" />
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<param name="collapse" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Collapse repeated locations onto single line with counts" />
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<conditional name="ins_out">
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<param name="include_ins_out" type="select" label="Include insertions output bed file?">
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<option value="true">Yes</option>
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<option value="false">No</option>
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</param>
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<when value="true" />
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<when value="false" />
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</conditional>
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<conditional name="del_out">
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<param name="include_del_out" type="select" label="Include deletions output bed file?">
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<option value="true">Yes</option>
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<option value="false">No</option>
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</param>
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<when value="true" />
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<when value="false" />
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</conditional>
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</inputs>
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<outputs>
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<data format="interval" name="output1" />
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<data format="bed" name="output2">
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<filter>ins_out[ "include_ins_out" ] == "true"</filter>
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</data>
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<data format="bed" name="output3">
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<filter>del_out[ "include_del_out" ] == "true"</filter>
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</data>
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</outputs>
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<tests>
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<test>
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<param name="input1" value="indel_sam2interval_in1.sam" ftype="sam"/>
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<param name="include_base" value="true"/>
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<param name="collapse" value="true"/>
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<param name="include_ins_out" value="true" />
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<param name="include_del_out" value="true" />
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<output name="output1" file="indel_sam2interval_out1.interval" ftype="interval"/>
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<output name="output2" file="indel_sam2interval_out2.bed" ftype="bed"/>
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<output name="output3" file="indel_sam2interval_out3.bed" ftype="bed"/>
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</test>
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</tests>
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<help>
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**What it does**
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Given a SAM file containing indels, converts these to an interval file with a column indicating whether it is an insertion or a deletion, and then also can create a BED file for each type (one for insertions, one for deletions). The interval file can be combined with other like files to create a table useful for analysis with the Indel Analysis Table tool. The BED files can be useful for visualizing the reads.
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-----
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**Example**
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Suppose you have the following mapping results::
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r327 16 chrM 11 37 8M1D10M * 0 0 CTTACCAGATAGTCATCA -+<2;?@BA@?-,.+4=4 XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:41^C35
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r457 0 chr1 14 37 14M * 0 0 ACCTGACAGATATC =/DF;?@1A@?-,. XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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r501 16 chrM 6 23 7M1I13M * 0 0 TCTGTGCCTACCAGACATTCA +=$2;?@BA@?-,.+4=4=4A XT:A:U NM:i:3 X0:i:1 X1:i:1 XM:i:2 XO:i:1 XG:i:1 MD:Z:28C36G9 XA:Z:chrM,+134263658,14M1I61M,4;
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r1288 16 chrM 8 37 11M1I7M * 0 0 TCACTTACCTGTACACACA /*F2;?@%A@?-,.+4=4= XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T0T1A69
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r1902 0 chr1 4 37 7M2D18M * 0 0 AGTCTCTTACCTGACGGTTATGA <2;?@BA@?-,.+4=4=4AA663 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0
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r2204 16 chrM 9 0 19M * 0 0 CTGGTACCTGACAGGTATC 2;?@BA@?-,.+4=4=4AA XT:A:R NM:i:1 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75 XA:Z:chrM,-564927,76M,1;
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r2314 16 chrM 6 37 10M2D8M * 0 0 TCACTCTTACGTCTGA <2;?@BA@?-,.+4=4 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:25A5^CA45
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r3001 0 chrM 13 37 3M1D5M2I7M * 0 0 TACAGTCACCCTCATCA <2;?@BA/(@?-,$& XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0
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r3218 0 chr1 13 37 8M1D7M * 0 0 TACAGTCACTCATCA <2;?@BA/(@?-,$& XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0
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r4767 16 chr2 3 37 15M2I7M * 0 0 CAGACTCTCTTACCAAAGACAGAC <2;?@BA/(@?-,.+4=4=4AA66 XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T1A4T65
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r5333 0 chrM 5 37 17M1D8M * 0 0 GTCTCTCATACCAGACAACGGCAT FB3$@BA/(@?-,.+4=4=4AA66 XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:45C10^C0C5C13
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r6690 16 chrM 7 23 20M * 0 0 CTCTCTTACCAGACAGACAT 2;?@BA/(@?-,.+4=4=4A XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 XA:Z:chrM,-568532,76M,1;
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r7211 0 chrM 7 37 24M * 0 0 CGACAGAGACAAAATAACATTTAA //<2;?@BA@?-,.+4=442;;6: XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:2 XO:i:1 XG:i:1 MD:Z:73G0G0
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r7899 69 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'#
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r9192 133 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&%
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r9922 16 chrM 4 0 7M3I9M * 0 0 CCAGACATTTGAAATCAGG F/D4=44^D++26632;;6 XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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r9987 16 chrM 4 0 9M1I18M * 0 0 AGGTTCTCATTACCTGACACTCATCTTG G/AD6"/+4=4426632;;6:<2;?@BA XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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r10145 16 chr1 16 0 5M2D7M * 0 0 CACATTGTTGTA G//+4=44=4AA XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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r10324 16 chrM 15 0 6M1D5M * 0 0 CCGTTCTACTTG A@??8.G//+4= XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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r12331 16 chrM 17 0 4M2I6M * 0 0 AGTCGAATACGTG 632;;6:<2;?@B XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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r12914 16 chr2 24 0 4M3I3M * 0 0 ACTACCCCAA G//+4=42,. XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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r13452 16 chrM 13 0 3M1D11M * 0 0 TACGTCACTCATCA IIIABCCCICCCCI XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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The following three files will be produced (Interval, Insertions BED and Deletions BED)::
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chr1 11 13 D - 1
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chr1 21 22 D - 1
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chr1 21 23 D - 1
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chr2 18 19 I AA 1
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chr2 28 29 I CCC 1
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chrM 11 12 I TTT 1
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chrM 13 14 I C 1
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chrM 13 14 I T 1
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chrM 16 17 D - 1
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chrM 16 18 D - 1
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chrM 19 20 D - 1
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chrM 19 20 I T 1
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chrM 21 22 D - 1
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chrM 21 22 I GA 1
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chrM 22 23 D - 1
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chr2 18 19
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chr2 28 29
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chrM 11 12
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chrM 13 14
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chrM 13 14
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chrM 19 20
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chrM 21 22
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chr1 11 13
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chr1 21 22
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chr1 21 23
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chrM 16 17
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chrM 16 18
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chrM 19 20
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chrM 21 22
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chrM 22 23
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For more information on SAM, please consult the `SAM format description`__.
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.. __: http://www.ncbi.nlm.nih.gov/pubmed/19505943
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</help>
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</tool>
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