running GATK or Mutect or a somatic variant caller individual chromosomes

[bogdan]

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tanasa • 10
United States

Dear all,


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

[yueluo]

Honestly, you might have better luck posting on GATK's forum.