running GATK or Mutect or a somatic variant caller individual chromosomes

Question

[Bogdan]

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