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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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Get forward and reverse reads supportting the allele depth(refand alt)，respectively #61

Open diushiguzhi opened 3 years ago

diushiguzhi commented 3 years ago

Hi,Dears,

How can I get forward and reverse reads supportting the allele depth(ref and alt)，respectively from vcf? For example，the FORMAT and Value below: GT:GQ:AD:DP:VF:NL:SB:NC:US:AQ:LQ 0/1:100:620,5496:6118:0.89833:30:-100.0000:0.0453:552,716,840,1290,874,1224,636,799,934,1428,977,1344:100.000:100.000

Thanks!

tamsen commented 3 years ago

try "-ReportRcCounts" and "OutputSBFiles" options. See https://github.com/Illumina/Pisces/wiki/Pisces-5.2.10-Supported-Options for more help.

Thanks for using pisces!