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VCFFixIndels
Pierre Lindenbaum edited this page Mar 23, 2015
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Fix samtools INDELS for @SolenaLS
See also Compilation
$ make vcffixindels| Option | Description |
|---|---|
| IN=File | VCF file to process. Default stdin. Default value: null. |
| OUT=File | VCF file to generate. Default stdout. Default value: null. |
$ java -jar dist/vcffixindels.jar I=input.vcf.gz | grep FIX
2 749862 . T TT 94.50 . AC1=2;AF1=1;DP=13;DP4=0,0,5,8;FQ=-73.5;INDEL;INDELFIXED=CTTTTTT|CTTTTTTT|74954856;IS=13,1.000000;MQ=50;VDB=4.019414e-04 GT:PL:DP:GQ 1/1:135,39,0:13:75
- "Unified Representation of Genetic Variants" http://bioinformatics.oxfordjournals.org/content/early/2015/02/19/bioinformatics.btv112.abstract
- Issue Tracker: http://github.com/lindenb/jvarkit/issues`
- Source Code: http://github.com/lindenb/jvarkit
##History
- 2015 : Creation
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