| Next changeset 1:a20ac5d90c16 (2018-08-10) |
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Commit message:
planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty |
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added:
extractSplitReads_BwaMem.xml test-data/JS01-BWA-MEM.splitters.out.sam test-data/JS01-BWA-MEM.splitters.sam test-data/pe.pos_sorted.out.sam test-data/pe.pos_sorted.sam |
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| 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 |
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| @@ -0,0 +1,109 @@ +<tool id="extractsplitreads_bwamem" + name="Extract Split Reads" + version="0.1.0"> + + <description>from bwaMEM (part of lumpy-sv)</description> + + <requirements> + <requirement type="package" version="0.2.14a">lumpy-sv</requirement> + </requirements> + + <!-- Not sure yet how to call the command if the lumpy-sv package in bioconda doesn't put the script in an executable location on PATH --> + + <version_command>extractSplitReads_BwaMem | grep ^extractSplitReads_BwaMem | cut -d v -f 2</version_command> + + <command detect_errors="aggressive"> + <![CDATA[ + extractSplitReads_BwaMem + -i '$input' + -n $numSplits + $includeDups + -m $minNonOverlap + > '$output' + ]]> + </command> + + <inputs> + + <param format="sam" name="input" type="data" label="Sam alignment file" argument="--infile"/> + + <param name="numSplits" + label="numSplits" + argument="--numSplits" + + type="integer" + value="2" + + help="The maximum number of split-read mappings to allow per read. Reads with more are excluded." /> + + <param name="includeDups" + label="includeDups" + argument="--includeDups" + + type="boolean" + truevalue="--includeDups" + falsevalue="" + checked="no" + value="false" + + help="Include alignments marked as duplicates." /> + + <param name="minNonOverlap" + label="minNonOverlap" + argument="--minNonOverlap" + + type="integer" + value="20" + + help="Minimum non-overlap between split alignments on the query." /> + + </inputs> + <outputs> + <data format="sam" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="JS01-BWA-MEM.splitters.sam"/> + <output name="output" file="JS01-BWA-MEM.splitters.out.sam"/> + </test> + <test> + <param name="input" value="pe.pos_sorted.sam"/> + <output name="output" file="pe.pos_sorted.out.sam"/> + </test> + </tests> + + <help> + <![CDATA[ + +Usage: `extractSplitReads_BwaMem -i <file>` + +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) + + ]]> + </help> + + <citations> + <citation type="doi">doi:10.1186/gb-2014-15-6-r84</citation> + </citations> + +</tool> |
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| 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 |
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| b'@@ -0,0 +1,15905 @@\n+@HD\tVN:1.3\tSO:coordinate\n+@SQ\tSN:1\tLN:3297305\n+@SQ\tSN:2\tLN:1806219\n+@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_\n+@PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL: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 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| diff -r 000000000000 -r 839c219ab0aa test-data/JS01-BWA-MEM.splitters.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JS01-BWA-MEM.splitters.sam Fri Aug 10 11:46:23 2018 -0400 |
| b |
| b'@@ -0,0 +1,15905 @@\n+@HD\tVN:1.3\tSO:coordinate\n+@SQ\tSN:1\tLN:3297305\n+@SQ\tSN:2\tLN:1806219\n+@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_\n+@PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL: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\n+JLK5VL1:1077:HFWVKBCXY:1:1103:1074:98134_2\t2064\t1\t1\t60\t39H36M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATATATATG\tIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD\tNM:i:0\tMD:Z:36\tAS:i:36\tXS:i:0\tSA:Z:1,3297267,-,39M36S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:1202:15123:38326_2\t2064\t1\t1\t60\t41H34M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATATATA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD\tNM:i:0\tMD:Z:34\tAS:i:34\tXS:i:0\tSA:Z:1,3297265,-,41M34S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:1209:16641:16186_2\t2064\t1\t1\t60\t44H31M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD\tNM:i:0\tMD:Z:31\tAS:i:31\tXS:i:0\tSA:Z:1,3297262,-,44M31S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:1212:11752:20298_2\t2064\t1\t1\t60\t44H31M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATAT\tIIIIIIIIIIIIIIIIIIIIIIIHHIDDDAD\tNM:i:0\tMD:Z:31\tAS:i:31\tXS:i:0\tSA:Z:1,3297262,-,44M31S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:1214:19672:47534_2\t2064\t1\t1\t60\t44H31M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATAT\tIIIIIIIHHFHHHHHIHEIHIHFGEH@DD0D\tNM:i:0\tMD:Z:31\tAS:i:31\tXS:i:0\tSA:Z:1,3297262,-,44M31S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:2101:14894:37824_2\t2064\t1\t1\t60\t39H36M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATATATATG\tHCIHHF@EGHHEIIHIIHEHG@HGFHGCCHID@DB<\tNM:i:0\tMD:Z:36\tAS:i:36\tXS:i:0\tSA:Z:1,3297267,-,39M36S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:2109:12740:40845_2\t2064\t1\t1\t60\t39H36M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATATATATG\tIIIIIIIIIIIIIIIHIIIIIHIIHIIIIIIDDDDD\tNM:i:0\tMD:Z:36\tAS:i:36\tXS:i:0\tSA:Z:1,3297267,-,36M39S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:2206:4207:62727_2\t2064\t1\t1\t60\t42H33M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATATAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD\tNM:i:0\tMD:Z:33\tAS:i:33\tXS:i:0\tSA:Z:1,3297264,-,42M33S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:2208:3802:52918_2\t2064\t1\t1\t60\t44H31M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATAT\tIIIIIIIIIIIIIIIIIIIIIIIHHIDDDDD\tNM:i:0\tMD:Z:31\tAS:i:31\tXS:i:0\tSA:Z:1,3297262,-,44M31S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:2210:10978:28070_2\t2064\t1\t1\t60\t39H36M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATATTTATG\tCFHCCHFHHEHFHEIIHCIHGCF?EHHHEFIDDABB\tNM:i:1\tMD:Z:31A4\tAS:i:31\tXS:i:0\tSA:Z:1,3297267,-,39M36S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:2216:3802:88555_2\t16\t1\t1\t60\t30S45M\t*\t0\t0\tGAAAATCGTTTTCTCGTTTTTCCGTTTTAGGCTTCAAGATAAATATATATAAGATCTATATATATGATCTTTTAT\t1IIIHFIHIIIIIIGHHIHHGIHIIIHIHHGHHHEIIIIIIHHHIIHIIIIHHHHIHIIIHIIIIHHHHHCDDD@\tNM:i:0\tMD:Z:45\tAS:i:45\tXS:i:0\tSA:Z:1,3297276,-,30M45S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:2:1105:12373:43168_2\t2064\t1\t1\t60\t39H36M\t*\t0\t0\tGCTTCAAGATAAATATATATAAGATCTATATATATG\tHIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIDDDDD\tNM:i:0\tMD:Z:36\tAS:i:36\tXS:i:0\tSA:Z:1,3297267,-,39M36S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5V'..b'ATCGCCTTAGAAA\tGEHH@F@GHHCCCG1IH@C1@?ECCCHDFD1HCD?DD<\tNM:i:1\tMD:Z:36C1\tAS:i:36\tXS:i:0\tSA:Z:1,1886238,-,37M38S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:2:1205:3473:72524_2\t0\t2\t1806027\t60\t48M27S\t*\t0\t0\tCTTCCAAAACAATCTCAATACGGTCAGCTTGAACTTGTTGCGTCAGCTGAGCTGACGCAACAAGTTCAAGCTGAC\tDDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHIIGIHIIIIIIHIIIIIIIIIIIIIGHFIHIHIIIGH\tNM:i:0\tMD:Z:48\tAS:i:48\tXS:i:0\tSA:Z:2,1806049,-,31M44S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:2:1106:18423:65345_2\t2048\t2\t1806047\t60\t45H30M\t*\t0\t0\tCGGTCAGCTTGAACTTGTTGCGTCAGCTCA\tIIIIIIIIIIIGIIHIIIIIIIIIIIIIII\tNM:i:0\tMD:Z:30\tAS:i:30\tXS:i:0\tSA:Z:2,1806177,+,43M32S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:2:1205:3473:72524_2\t2064\t2\t1806049\t60\t31M44H\t*\t0\t0\tGTCAGCTTGAACTTGTTGCGTCAGCTCAGCT\tHGIIIHIHIFHGIIIIIIIIIIIIIHIIIII\tNM:i:0\tMD:Z:31\tAS:i:31\tXS:i:0\tSA:Z:2,1806027,+,48M27S,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:2:1208:5966:58603_2\t0\t2\t1806175\t60\t45M30S\t*\t0\t0\tCAACAAAAAGGTGCACATTCATTTTGAACAACCATCACATAAAAAACCATCAAAATTGGCTGTTTTATGATTTAA\tDDDDDIIIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHIIIIHIIIIIIIIIIIIIHEHHHIIIHIIIII\tNM:i:0\tMD:Z:45\tAS:i:45\tXS:i:0\tSA:Z:2,1,+,45S30M,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:2206:8089:41069_2\t0\t2\t1806177\t60\t43M32S\t*\t0\t0\tACAAAAAGGTGCACATTCATTTTGAACAACCATCACATAAAAAACCATCAAAATTGGCTGTTTTATGATTTAAGA\tDDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIHIIIIIIIIIIIIIHIIIIIIIIFHIIHHHI\tNM:i:0\tMD:Z:43\tAS:i:43\tXS:i:0\tSA:Z:2,1,+,43S32M,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:2:1106:18423:65345_2\t0\t2\t1806177\t60\t43M32S\t*\t0\t0\tACAAAAAGGTGCACATTCATTTTGAACAACCATCACATAAAAAACCGGTCAGCTTGAACTTGTTGCGTCAGCTCA\tDDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIHIIIIIIIIIIIIIII\tNM:i:0\tMD:Z:43\tAS:i:43\tXS:i:0\tSA:Z:2,1806047,+,45S30M,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:2:2111:9537:52502_2\t0\t2\t1806177\t60\t43M32S\t*\t0\t0\tACAAAAAGGTGCACATTCATTTTGAACAACCATCACATAAAAAACCATCAAAATTGGCTGTTTTATGATTTAAGA\tD0DA@EHIHIEHIIIIIIIIIIIHHIIGHHIIIIIIIIIIEHIIIIIIHFHHII1@@GHHCHHHHIHHEHHIIHH\tNM:i:0\tMD:Z:43\tAS:i:43\tXS:i:0\tSA:Z:2,1,+,43S32M,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:1214:19103:63679_2\t0\t2\t1806180\t60\t40M35S\t*\t0\t0\tAAAAGGTGCACATTCATTTTGAACAACCATCACATAAAAAACCATCAAAATTGGCTGTTTTATGATTTAAGAAGA\tDDDDDIIIIIIIIIIIIIHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIHHHHIHIGEHIHIIIIIH\tNM:i:0\tMD:Z:40\tAS:i:40\tXS:i:0\tSA:Z:2,1,+,40S35M,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:2:2204:19153:3663_2\t0\t2\t1806180\t60\t40M35S\t*\t0\t0\tAAAAGGTGCACATTCATTTTGAACAACCATCACATAAAAAACCATCAAAATTGGCTGTTTTATGATTTAAGAAGA\tDDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHIIIIIIIIIIIIIIII\tNM:i:0\tMD:Z:40\tAS:i:40\tXS:i:0\tSA:Z:2,1,+,40S35M,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:1115:9214:73605_2\t2064\t2\t1806184\t60\t36M39H\t*\t0\t0\tGGTGCACATTCATTTTGAACAACCATCACATAAAAA\tIIIIIIIIIIIHIIIIHIIIIHHIIIIIIIIIIIII\tNM:i:0\tMD:Z:36\tAS:i:36\tXS:i:0\tSA:Z:2,1,-,36S39M,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:2:2116:5416:35804_2\t2064\t2\t1806187\t60\t33M42H\t*\t0\t0\tGCACATTCATTTTGAACAACCATCACATAAAAA\tHHIIIIIGIIIIIIIIIIIIIHIHIIIIIIIIH\tNM:i:0\tMD:Z:33\tAS:i:33\tXS:i:0\tSA:Z:2,1,-,33S42M,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n+JLK5VL1:1077:HFWVKBCXY:1:1106:4583:45850_2\t2048\t2\t1806190\t60\t30M45H\t*\t0\t0\tCATTCATTTTGAACAACCATCACATAAAAA\tDDDDDIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tMD:Z:30\tAS:i:30\tXS:i:0\tSA:Z:2,1,+,30S45M,60,0;\tRG:Z:justin_-_Barcode_Splitter_on_data_26__data_25__and_data_23__JS-01_\n' |
| b |
| diff -r 000000000000 -r 839c219ab0aa test-data/pe.pos_sorted.out.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pe.pos_sorted.out.sam Fri Aug 10 11:46:23 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +@HD VN:1.3 SO:coordinate +@SQ SN:chr10 LN:135534747 +@PG ID:bwa PN:bwa VN:0.5.9-r16 |
| b |
| diff -r 000000000000 -r 839c219ab0aa test-data/pe.pos_sorted.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pe.pos_sorted.sam Fri Aug 10 11:46:23 2018 -0400 |
| b |
| b'@@ -0,0 +1,5000 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_418872_419339_1:0:0_4:0:0_a2797\t147\tchr10\t428090\t60\t150M\t=\t427772\t-468\t*\t*\tXT:A:U\tNM:i:4\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tMD:Z:60A34A22T22G8\n+chr10_418888_419391_3:0:0_4:0:0_21f43\t147\tchr10\t428142\t60\t150M\t=\t427788\t-504\t*\t*\tXT:A:U\tNM:i:4\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tMD:Z:61G7C2T38C38\n+chr10_418968_419443_3:0:0_3:0:0_34707\t147\tchr10\t428194\t60\t150M\t=\t427868\t-476\t*\t*\tXT:A:U\tNM:i:3\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:69A43A4A31\n+chr10_418983_419529_2:0:0_3:0:0_b98dd\t83\tchr10\t428280\t60\t150M\t=\t427883\t-547\t*\t*\tXT:A:U\tNM:i:3\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:67C34C45T1\n+chr10_419111_419609_6:0:0_3:0:0_4f9c2\t147\tchr10\t428360\t60\t150M\t=\t428011\t-499\t*\t*\tXT:A:U\tNM:i:3\tSM:i:37\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:15C63A30T39\n+chr10_419491_419916_2:0:0_2:0:0_c8bfe\t163\tchr10\t428391\t60\t150M\t=\t428667\t426\t*\t*\tXT:A:U\tNM:i:2\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:3T89C56\n+chr10_419168_419647_3:0:0_3:0:0_890a0\t147\tchr10\t428398\t60\t150M\t=\t428068\t-480\t*\t*\tXT:A:U\tNM:i:3\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:71G55C1C20\n+chr10_419512_420069_2:0:0_3:0:0_d70d1\t163\tchr10\t428412\t60\t150M\t=\t428820\t558\t*\t*\tXT:A:U\tNM:i:2\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:33A56C59\n+chr10_419132_419705_2:0:0_4:0:0_93539\t83\tchr10\t428456\t60\t150M\t=\t428032\t-574\t*\t*\tXT:A:U\tNM:i:4\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tMD:Z:4T29C9A82G22\n+chr10_419621_420088_2:0:0_6:0:0_98684\t99\tchr10\t428521\t60\t150M\t=\t428839\t468\t*\t*\tXT:A:U\tNM:i:2\tSM:i:37\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:22G79G47\n+chr10_419491_419916_2:0:0_2:0:0_c8bfe\t83\tchr10\t428667\t60\t150M\t=\t428391\t-426\t*\t*\tXT:A:U\tNM:i:2\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:69A73A6\n+chr10_419783_420341_10:0:0_5:0:0_2fe2a\t99\tchr10\t428685\t29\t2S148M\t=\t429092\t557\t*\t*\tXT:A:M\tNM:i:9\tSM:i:29\tAM:i:29\tXM:i:9\tXO:i:0\tXG:i:0\tMD:Z:20G3G1A8A16A7G0A29G39C16\n+chr10_419512_420069_2:0:0_3:0:0_d70d1\t83\tchr10\t428820\t60\t150M\t=\t428412\t-558\t*\t*\tXT:A:U\tNM:i:3\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:19T1A63C64\n+chr10_419621_420088_2:0:0_6:0:0_98684\t147\tchr10\t428839\t60\t150M\t=\t428521\t-468\t*\t*\tXT:A:U\tNM:i:6\tSM:i:25\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:6\tXO:i:0\tXG:i:0\tMD:Z:18T2A73A22C11C5T13\n+chr10_419940_420373_4:0:0_3:0:0_b369\t163\tchr10\t428840\t60\t150M\t=\t429124\t434\t*\t*\tXT:A:U\tNM:i:4\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tMD:Z:1A46A45A23T31\n+chr10_419964_420481_0:0:0_2:0:0_65b5c\t163\tchr10\t428864\t60\t150M\t=\t429232\t518\t*\t*\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:150\n+chr10_419783_420341_10:0:0_5:0:0_2fe2a\t147\tchr10\t429092\t29\t150M\t=\t428685\t-557\t*\t*\tXT:A:U\tNM:i:5\tSM:i:29\tAM:i:29\tX0:i:1\tX1:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tMD:Z:7C9T61A56A8C4\n+chr10_419940_420373_4:0:0_3:0:0_b369\t83\tchr10\t429124\t60\t150M\t=\t428840\t-434\t*\t*\tXT:A:U\tNM:i:3\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:94A11G37G5\n+chr10_420252_420777_3:0:0_2:0:0_b419a\t99\tchr10\t429152\t60\t150M\t=\t429528\t526\t*\t*\tXT:A:U\tNM:i:3\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:94A1C43C9\n+chr10_419964_420481_0:0:0_2:0:0_65b5c\t83\tchr10\t429232\t60\t150M\t=\t428864\t-518\t*\t*\tXT:A:U\tNM:i:2\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:18G105A25\n+chr10_420374_420927_4:0:0_2:1:0_589ef\t163\tchr10\t429274\t60\t150M\t=\t429678\t554\t*\t*\tXT:A:U\tNM:i:4\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tMD:Z:42C68T17G1A18\n+chr10_420527_421050_3:0:0_1:0:0_a02c2\t163\tchr10\t429427\t60\t150M\t=\t429801\t524\t*\t*\tXT:A:U\tNM:i:3\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:44G14A62A27\n' |