Is it ok to use -L for each chromosome separately when running Mutect2?

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Xuning Wang

• January 30, 2023 21:41

Hi,

In order to speed up Mutect2, it is OK to run it with -L on each chromosome, such as -L  chr1:1-248956422 for hg38? Will VCF results for a chromosome be the same as you would get if run with whole genome? How to combine the VCF files of each chromosome, and generate the .vcf.stats file for the combined result?

Thank you!

Jason

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  David Benjamin

  • February 06, 2023 18:19

  Xuning Wang Sure, that approach is fine and will give the same results as calling on the whiole genome.  The stats files can be combined with `MergeMutectStats`.  This is the exactly the approach that the official Mutect2 WDL in the GATK github repo uses.

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