Variant calling for matched samples

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Shivangi Agarwal

• January 05, 2022 21:40

Hi,

I want to call variants for my 36 samples each of which is having normal data. The samples are matched normal.

Please let me know how to correctly run GATK and what are the steps for this ?

My GATK version is 4.2.2.0.

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  Shivangi Agarwal

  • January 07, 2022 20:03

  Hey Genevieve Brandt,

  Can you please spare some time to answer my query as mentioned above ? I need to run this analysis at the earliest.

   

   

  Thanks and regards

  Shivangi Agarwal

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  Genevieve Brandt (she/her)

  • January 10, 2022 16:56

  Shivangi Agarwal please see our support policy here: https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines

  We answer questions in the order they are recieved.

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  Genevieve Brandt (she/her)

  • January 11, 2022 18:35

  Hi Shivangi Agarwal,

  I can help to figure out the steps necessary to run your analysis! We have a best practices article for somatic short variant discovery, which outlines the steps that you should run to get results with your data. Each sample and normal pair should be run through this pipeline individually (unless the samples are from the same individual). Having normals for all your samples is excellent because you will get the best results in tumor-normal mode. Your Mutect2 command will look like this:

  gatk Mutect2 \
       -R reference.fa \
       -I tumor.bam \
       -I normal.bam \
       -normal normal_sample_name \
       --germline-resource af-only-gnomad.vcf.gz \
       --panel-of-normals pon.vcf.gz \
       -O somatic.vcf.gz

  You can find this command and more information about Mutect2 in the tool docs page and also our tutorial article as well. 

  Please let me know if you have further questions.

  Best,

  Genevieve

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