Entering edit mode
8.1 years ago
Bogdan
★
1.4k
Dear all,
We are using GATK/Mutect, Strelka, SomaticSnipper or VarScan for calling the somatic mutations.
In GATK/Mutect, we can run the pipeline on each chromosome at a time (-L
option).
Please could you advise on how I could design a somatic variant calling pipeline to run on all the chromosomes at once? What is the most efficient way to specify that?
Possibly to run a chromosome on a microprocessor? Or in any other way?
Thanks a lot,
bogdan