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Old 02-09-2016, 04:41 PM   #1
bogdan
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Default running GATK or Mutect or a somatic variant caller individual chromosomes

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tanasa 10
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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
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Old 10-08-2016, 11:49 PM   #2
yueluo
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Honestly, you might have better luck posting on GATK's forum.
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