# HG changeset patch # User hepcat72 # Date 1533915983 14400 # Node ID 839c219ab0aa62cb6ea44036c0bf80c867713096 planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty diff -r 000000000000 -r 839c219ab0aa extractSplitReads_BwaMem.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extractSplitReads_BwaMem.xml Fri Aug 10 11:46:23 2018 -0400 @@ -0,0 +1,109 @@ + + + from bwaMEM (part of lumpy-sv) + + + lumpy-sv + + + + + extractSplitReads_BwaMem | grep ^extractSplitReads_BwaMem | cut -d v -f 2 + + + '$output' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ` + +extractSplitReads_BwaMem v0.1.0 + +Author: Ira Hall + +Description: Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates. + +Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405. + + +Options: + -h, --help show this help message and exit + -i FILE, --inFile=FILE + A SAM file or standard input (-i stdin). + -n INT, --numSplits=INT + The maximum number of split-read mappings to allow per + read. Reads with more are excluded. Default=2 + -d, --includeDups Include alignments marked as duplicates. Default=False + -m INT, --minNonOverlap=INT + minimum non-overlap between split alignments on the + query (default=20) + + ]]> + + + + doi:10.1186/gb-2014-15-6-r84 + + + diff -r 000000000000 -r 839c219ab0aa test-data/JS01-BWA-MEM.splitters.out.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JS01-BWA-MEM.splitters.out.sam Fri Aug 10 11:46:23 2018 -0400 @@ -0,0 +1,15905 @@ +@HD VN:1.3 SO:coordinate +@SQ SN:1 LN:3297305 +@SQ SN:2 LN:1806219 +@RG ID:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ SM:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ PL:ILLUMINA LB:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +@PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 6 -v 1 -R @RG\tID:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\tSM:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\tPL:ILLUMINA\tLB:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ localref.fa /galaxy/files/000/250/dataset_250169.dat +JLK5VL1:1077:HFWVKBCXY:1:1103:1074:98134_2_2 2064 1 1 60 39H36M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATATG IIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD NM:i:0 MD:Z:36 AS:i:36 XS:i:0 SA:Z:1,3297267,-,39M36S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:1202:15123:38326_2_2 2064 1 1 60 41H34M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD NM:i:0 MD:Z:34 AS:i:34 XS:i:0 SA:Z:1,3297265,-,41M34S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:1209:16641:16186_2_2 2064 1 1 60 44H31M * 0 0 GCTTCAAGATAAATATATATAAGATCTATAT IIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD NM:i:0 MD:Z:31 AS:i:31 XS:i:0 SA:Z:1,3297262,-,44M31S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:1212:11752:20298_2_2 2064 1 1 60 44H31M * 0 0 GCTTCAAGATAAATATATATAAGATCTATAT IIIIIIIIIIIIIIIIIIIIIIIHHIDDDAD NM:i:0 MD:Z:31 AS:i:31 XS:i:0 SA:Z:1,3297262,-,44M31S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:1214:19672:47534_2_2 2064 1 1 60 44H31M * 0 0 GCTTCAAGATAAATATATATAAGATCTATAT IIIIIIIHHFHHHHHIHEIHIHFGEH@DD0D NM:i:0 MD:Z:31 AS:i:31 XS:i:0 SA:Z:1,3297262,-,44M31S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:2101:14894:37824_2_2 2064 1 1 60 39H36M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATATG HCIHHF@EGHHEIIHIIHEHG@HGFHGCCHID@DB< NM:i:0 MD:Z:36 AS:i:36 XS:i:0 SA:Z:1,3297267,-,39M36S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:2109:12740:40845_2_2 2064 1 1 60 39H36M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATATG IIIIIIIIIIIIIIIHIIIIIHIIHIIIIIIDDDDD NM:i:0 MD:Z:36 AS:i:36 XS:i:0 SA:Z:1,3297267,-,36M39S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:2206:4207:62727_2_2 2064 1 1 60 42H33M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD NM:i:0 MD:Z:33 AS:i:33 XS:i:0 SA:Z:1,3297264,-,42M33S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:2208:3802:52918_2_2 2064 1 1 60 44H31M * 0 0 GCTTCAAGATAAATATATATAAGATCTATAT IIIIIIIIIIIIIIIIIIIIIIIHHIDDDDD NM:i:0 MD:Z:31 AS:i:31 XS:i:0 SA:Z:1,3297262,-,44M31S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:2210:10978:28070_2_2 2064 1 1 60 39H36M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATTTATG CFHCCHFHHEHFHEIIHCIHGCF?EHHHEFIDDABB NM:i:1 MD:Z:31A4 AS:i:31 XS:i:0 SA:Z:1,3297267,-,39M36S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:1:2216:3802:88555_2_2 16 1 1 60 30S45M * 0 0 GAAAATCGTTTTCTCGTTTTTCCGTTTTAGGCTTCAAGATAAATATATATAAGATCTATATATATGATCTTTTAT 1IIIHFIHIIIIIIGHHIHHGIHIIIHIHHGHHHEIIIIIIHHHIIHIIIIHHHHIHIIIHIIIIHHHHHCDDD@ NM:i:0 MD:Z:45 AS:i:45 XS:i:0 SA:Z:1,3297276,-,30M45S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:1105:12373:43168_2_2 2064 1 1 60 39H36M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATATG HIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD NM:i:0 MD:Z:36 AS:i:36 XS:i:0 SA:Z:1,3297267,-,39M36S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:1109:12651:88047_2_2 2064 1 1 60 44H31M * 0 0 GCTTCAAGATAAATATATATAAGATCTATAT IIIIIIIIIIIIIIIIIIIIIIIIHIDDDDD NM:i:0 MD:Z:31 AS:i:31 XS:i:0 SA:Z:1,3297262,-,44M31S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:1207:11834:6072_2_2 2064 1 1 60 41H34M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATA IIIIIHIHHIIIIIIIIIIIIIIHIIIIIDDDDD NM:i:0 MD:Z:34 AS:i:34 XS:i:0 SA:Z:1,3297265,-,41M34S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:1208:8396:75381_2_2 16 1 1 60 35S40M * 0 0 AGAGAGAAAATCGTTTTCTCGTTTTTCCGTTTTAGGCTTCAAGATAAATATATATAAGATCTATATATATGATCT GIHIIIIIIIIHIIIIIGGIHIHHGHFHFIIIIIHCHHHIIHIIIIIIHIHIIIIIIHHEIHIIIIIIHE@DDDD NM:i:0 MD:Z:40 AS:i:40 XS:i:0 SA:Z:1,3297271,-,35M40S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:2101:20263:4509_2_2 2064 1 1 60 44H31M * 0 0 GCTTCAAGATAAATATATATAAGATCTATAT HIIIIIIIIIIIIIIIIIIIIIIHHIDDDDD NM:i:0 MD:Z:31 AS:i:31 XS:i:0 SA:Z:1,3297262,-,44M31S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:2103:12787:34005_2_2 2064 1 1 60 41H34M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATA IIIIIIIIIIIIIIIIIIIIIIIHIIIIIDDDDD NM:i:0 MD:Z:34 AS:i:34 XS:i:0 SA:Z:1,3297265,-,41M34S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:2106:12332:53183_2_2 2064 1 1 60 40H35M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD NM:i:0 MD:Z:35 AS:i:35 XS:i:0 SA:Z:1,3297266,-,40M35S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:2111:18151:46065_2_2 16 1 1 60 30S45M * 0 0 GAAAATCGTTTTCTCGTTTTTCCGTTTTAGGCTTCAAGATAAATATATATAAGATCTATATATATGATCTTTTAT EIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDAD NM:i:0 MD:Z:45 AS:i:45 XS:i:0 SA:Z:1,3297276,-,30M45S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:2112:20688:100425_2_2 16 1 1 60 35S40M * 0 0 AGAGAGGAAATCGTTTTCTCGTTTTTCCGTTTTAGGCTTCAAGATAGATATATATAAGATCTATATATATGATCT HIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD NM:i:1 MD:Z:11A28 AS:i:35 XS:i:0 SA:Z:1,3297271,-,35M40S,59,1; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:2208:4093:12502_2_2 2064 1 1 60 44H31M * 0 0 GCTTCAAGATAAATATATATAAGATCTATAT GIIIHIIIIIIIIIIIIIIIIIHHIIDDDDD NM:i:0 MD:Z:31 AS:i:31 XS:i:0 SA:Z:1,3297262,-,44M31S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:2211:18567:41993_2_2 16 1 1 60 36S39M * 0 0 CAGAGAGAAAATCGTTTTCTCGTTTTTCCGTTTTAGGCTTCAAGATAAATATATATAAGATCTATATATATGATC IIIIIIIIHGGIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHGIIIIIIIIIIIIIIIHHIHIIDDDDD NM:i:0 MD:Z:39 AS:i:39 XS:i:0 SA:Z:1,3297270,-,36M39S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:2212:5101:94756_2_2 2064 1 1 60 40H35M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATAT GHIIHHHIHIHHHIIIIIIIHHGIIIGHIIBD@?D NM:i:0 MD:Z:35 AS:i:35 XS:i:0 SA:Z:1,3297266,-,40M35S,60,0; RG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_ +JLK5VL1:1077:HFWVKBCXY:2:2215:7722:21443_2_2 2064 1 1 60 41H34M * 0 0 GCTTCAAGATAAATATATATAAGATCTATATATA IIHCIIIIHEIIIHIIIIIIHIIHIIHGC