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,