HaplotypeCaller vcf file analysis

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ziliang

• November 23, 2020 14:18

Hi, how can i analyze the vcf file after using HaplotypeCaller? What is the counting of SNPs for and how can i compare it with the assembly size?

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  Genevieve Brandt (she/her)

  • November 24, 2020 18:39

  Hi ziliang,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

  For context, check out our support policy.

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  Pamela Bretscher

  • July 08, 2021 14:56

  Please see our HaplotypeCaller documentation in the tool index as well as this article on understanding/analyzing a VCF file: https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format

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