Entering edit mode
2.3 years ago
accdg2022
•
0
Hello,
Why when I run PISCES (after getting the realigned BAM file with GEMINI) does it report the VAFs with commas instead of dots? In this example, it should report 0.55. I have already check that it was not a bug from my text editor by opening it with vim:
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!
