[2] | 1 | <tool id="indel_sam2interval" name="Extract indels" version="1.0.0"> |
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| 2 | <description>from SAM</description> |
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| 3 | <command interpreter="python"> |
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| 4 | indel_sam2interval.py |
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| 5 | --input=$input1 |
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| 6 | --include_base=$include_base |
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| 7 | --collapse=$collapse |
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| 8 | --int_out=$output1 |
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| 9 | #if $ins_out.include_ins_out == "true" |
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| 10 | --bed_ins_out=$output2 |
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| 11 | #else |
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| 12 | --bed_ins_out="None" |
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| 13 | #end if |
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| 14 | #if $del_out.include_del_out == "true" |
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| 15 | --bed_del_out=$output3 |
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| 16 | #else |
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| 17 | --bed_del_out="None" |
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| 18 | #end if |
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| 19 | </command> |
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| 20 | <inputs> |
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| 21 | <param format="sam" name="input1" type="data" label="Select dataset to convert" /> |
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| 22 | <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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| 23 | <param name="collapse" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Collapse repeated locations onto single line with counts" /> |
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| 24 | <conditional name="ins_out"> |
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| 25 | <param name="include_ins_out" type="select" label="Include insertions output bed file?"> |
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| 26 | <option value="true">Yes</option> |
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| 27 | <option value="false">No</option> |
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| 28 | </param> |
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| 29 | <when value="true" /> |
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| 30 | <when value="false" /> |
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| 31 | </conditional> |
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| 32 | <conditional name="del_out"> |
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| 33 | <param name="include_del_out" type="select" label="Include deletions output bed file?"> |
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| 34 | <option value="true">Yes</option> |
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| 35 | <option value="false">No</option> |
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| 36 | </param> |
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| 37 | <when value="true" /> |
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| 38 | <when value="false" /> |
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| 39 | </conditional> |
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| 40 | </inputs> |
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| 41 | <outputs> |
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| 42 | <data format="interval" name="output1" /> |
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| 43 | <data format="bed" name="output2"> |
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| 44 | <filter>ins_out[ "include_ins_out" ] == "true"</filter> |
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| 45 | </data> |
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| 46 | <data format="bed" name="output3"> |
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| 47 | <filter>del_out[ "include_del_out" ] == "true"</filter> |
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| 48 | </data> |
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| 49 | </outputs> |
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| 50 | <tests> |
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| 51 | <test> |
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| 52 | <param name="input1" value="indel_sam2interval_in1.sam" ftype="sam"/> |
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| 53 | <param name="include_base" value="true"/> |
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| 54 | <param name="collapse" value="true"/> |
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| 55 | <param name="include_ins_out" value="true" /> |
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| 56 | <param name="include_del_out" value="true" /> |
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| 57 | <output name="output1" file="indel_sam2interval_out1.interval" ftype="interval"/> |
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| 58 | <output name="output2" file="indel_sam2interval_out2.bed" ftype="bed"/> |
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| 59 | <output name="output3" file="indel_sam2interval_out3.bed" ftype="bed"/> |
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| 60 | </test> |
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| 61 | </tests> |
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| 62 | <help> |
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| 63 | |
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| 64 | **What it does** |
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| 65 | |
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| 66 | 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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| 67 | |
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| 68 | ----- |
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| 69 | |
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| 70 | **Example** |
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| 71 | |
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| 72 | Suppose you have the following mapping results:: |
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| 73 | |
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| 74 | 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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| 75 | 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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| 76 | r501 16 chrM 6 23 7M1I13M * 0 0 TCTGTGCCTACCAGACATTCA +=$2;?@BA@?-,.+4=4=4A XT:A:U NM:i:3 X0:i:1 X1:i:1 XM:i:2 XO:i:1 XG:i:1 MD:Z:28C36G9 XA:Z:chrM,+134263658,14M1I61M,4; |
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| 77 | r1288 16 chrM 8 37 11M1I7M * 0 0 TCACTTACCTGTACACACA /*F2;?@%A@?-,.+4=4= XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T0T1A69 |
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| 78 | r1902 0 chr1 4 37 7M2D18M * 0 0 AGTCTCTTACCTGACGGTTATGA <2;?@BA@?-,.+4=4=4AA663 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0 |
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| 79 | r2204 16 chrM 9 0 19M * 0 0 CTGGTACCTGACAGGTATC 2;?@BA@?-,.+4=4=4AA XT:A:R NM:i:1 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75 XA:Z:chrM,-564927,76M,1; |
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| 80 | r2314 16 chrM 6 37 10M2D8M * 0 0 TCACTCTTACGTCTGA <2;?@BA@?-,.+4=4 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:25A5^CA45 |
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| 81 | r3001 0 chrM 13 37 3M1D5M2I7M * 0 0 TACAGTCACCCTCATCA <2;?@BA/(@?-,$& 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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| 82 | r3218 0 chr1 13 37 8M1D7M * 0 0 TACAGTCACTCATCA <2;?@BA/(@?-,$& XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0 |
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| 83 | r4767 16 chr2 3 37 15M2I7M * 0 0 CAGACTCTCTTACCAAAGACAGAC <2;?@BA/(@?-,.+4=4=4AA66 XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T1A4T65 |
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| 84 | r5333 0 chrM 5 37 17M1D8M * 0 0 GTCTCTCATACCAGACAACGGCAT FB3$@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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| 85 | 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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| 86 | 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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| 87 | r7899 69 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'# |
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| 88 | r9192 133 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&% |
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| 89 | 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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| 90 | 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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| 91 | 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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| 92 | 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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| 93 | 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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| 94 | 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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| 95 | 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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| 96 | |
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| 97 | |
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| 98 | The following three files will be produced (Interval, Insertions BED and Deletions BED):: |
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| 99 | |
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| 100 | chr1 11 13 D - 1 |
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| 101 | chr1 21 22 D - 1 |
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| 102 | chr1 21 23 D - 1 |
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| 103 | chr2 18 19 I AA 1 |
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| 104 | chr2 28 29 I CCC 1 |
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| 105 | chrM 11 12 I TTT 1 |
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| 106 | chrM 13 14 I C 1 |
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| 107 | chrM 13 14 I T 1 |
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| 108 | chrM 16 17 D - 1 |
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| 109 | chrM 16 18 D - 1 |
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| 110 | chrM 19 20 D - 1 |
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| 111 | chrM 19 20 I T 1 |
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| 112 | chrM 21 22 D - 1 |
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| 113 | chrM 21 22 I GA 1 |
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| 114 | chrM 22 23 D - 1 |
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| 115 | |
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| 116 | chr2 18 19 |
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| 117 | chr2 28 29 |
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| 118 | chrM 11 12 |
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| 119 | chrM 13 14 |
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| 120 | chrM 13 14 |
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| 121 | chrM 19 20 |
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| 122 | chrM 21 22 |
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| 123 | |
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| 124 | chr1 11 13 |
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| 125 | chr1 21 22 |
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| 126 | chr1 21 23 |
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| 127 | chrM 16 17 |
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| 128 | chrM 16 18 |
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| 129 | chrM 19 20 |
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| 130 | chrM 21 22 |
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| 131 | chrM 22 23 |
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| 132 | |
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| 133 | For more information on SAM, please consult the `SAM format description`__. |
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| 134 | |
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| 135 | .. __: http://www.ncbi.nlm.nih.gov/pubmed/19505943 |
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| 136 | |
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| 137 | |
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| 138 | </help> |
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| 139 | </tool> |
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