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VCFFixIndels
Pierre Lindenbaum edited this page Oct 30, 2013
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16 revisions
Fix samtools INDELS for @SolenaLS
See also Compilation
ant 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