Hello,

Why when I run PISCES (after getting the BAM file with GEMINI) does it report the VAFs with commas instead of dots? In this example, it should report 0.55.

GT:GQ:AD:DP:VF:NL:SB 0/1:43:155,9:164:0,55:20:-14,2244

The code used would be:

bashArguments = "Pisces -bam "+bamGemini+" -g "+refGenomeFolder+" -i "+targetBedFileIntervalList+" -UseStitchedXD TRUE -CallMNVs TRUE -MinBQ 30 -MinVF 0. 001 -MinMQ 10 --OutFolder "+outDir+"/pisces/pisces/"+sample+" --MaxNumThreads "+cpus

Thank you very much!