Question: running GATK or Mutect or a somatic variant caller individual chromosomes
gravatar for Bogdan
5.0 years ago by
Palo Alto, CA, USA
Bogdan1.1k wrote:

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,


sequencing snp genome • 2.3k views
ADD COMMENTlink written 5.0 years ago by Bogdan1.1k
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