Mutect2, force-calling-mode, and restricting calls to positions in force-call-alleles.vcf

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Robert Dubin

• July 28, 2020 20:27

Can you please provide
a) GATK version used  v4.1.7.0
b) Exact GATK commands used
c) The entire error log if applicable.

I am using GATK v4.1.7.0 and I am interested in running Mutect2 with an alleles file (force-call-alleles.vcf). In the example on the web site which shows an example of the use of the --alleles parameter, it states that the force-calls mode calls alleles in the force-call-alleles.vcf in addition to any other variants Mutect2 discovers. Is it possible, however, to restrict the output to variants ONLY present within the force-call-alleles.vcf  file?

 

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  Genevieve Brandt (she/her)

  • July 28, 2020 21:56

  Would the -L parameter work? You can use a VCF file as the interval for the tool to operate.

  Intervals and Interval Lists: https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists

  Mutect2 parameters: https://gatk.broadinstitute.org/hc/en-us/articles/360045800552-Mutect2

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  Robert Dubin

  • July 29, 2020 13:18

  Thank you very much for the suggestion. I just tried using Mutect2 with the -L parameter, and supplying it with a vcf file. It worked perfectly. Only the positions in the vcf file were examined. 

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  Genevieve Brandt (she/her)

  • July 29, 2020 16:10

  Thanks for posting your solution Robert Dubin! Glad it worked.

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