Getting HaplotypeCaller SNP support in tumor

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vctrymao

• January 20, 2021 22:01

I have a list of germline SNPs from HaplotypeCaller. I want to get the read level information, etc. of these SNPs in the tumor BAM file and format it into a VCF (ie. to see the read level support for the germline SNPs in the tumor sample, to be used for CNV calling). Is there an easy way to do this with GATK? 

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  Genevieve Brandt (she/her)

  • January 22, 2021 19:24

  Hi vctrymao - thanks for writing in.

  Our GATK Support Team is focused on resolving requests regarding abnormal results and GATK bugs/error messages. 

  For these type of questions, we ask that the community jumps in and contributes their knowledge of GATK. 

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  Genevieve Brandt (she/her)

  • February 08, 2021 23:00

  Hi vctrymao,

  I believe this tutorial might be what you are looking for: https://gatk.broadinstitute.org/hc/en-us/articles/360035890011--How-to-part-II-Sensitively-detect-copy-ratio-alterations-and-allelic-segments

  Does that help?

  Best,

  Genevieve

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