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Old 02-09-2016, 04:41 PM   #1
Location: san diego

Join Date: Jul 2008
Posts: 35
Default running GATK or Mutect or a somatic variant caller individual chromosomes

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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 is offline   Reply With Quote
Old 10-08-2016, 11:49 PM   #2
Location: Guangzhou China

Join Date: Aug 2013
Posts: 82

Honestly, you might have better luck posting on GATK's forum.
yueluo is offline   Reply With Quote

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