Unix pipe support and SAM fields used in Variant Calling pipeline

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Rocco Gabriele Storace

• November 19, 2020 13:38

Hi,

I'm new in GATK pipeline. Actually I'm studying GATK best practices concerning the Variant Calling pipeline. I am curious to know if the markduplicates / applyBQSR / haplotypecaller tools:

1. support the Unix pipe, in order to optimize the processing

2. use all the fields specified in the SAM format or only needs some specific fields (SAM)

Thanks for the help,

Rocco

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  Genevieve Brandt (she/her)

  • November 19, 2020 22:13

  Hi Rocco Gabriele Storace,

  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 15:07

  Please see our tool index documentation for these tools:

  https://gatk.broadinstitute.org/hc/en-us/articles/360036358972-MarkDuplicatesSpark

  https://gatk.broadinstitute.org/hc/en-us/articles/360036346652-ApplyBQSR

  https://gatk.broadinstitute.org/hc/en-us/articles/360042913231-HaplotypeCaller

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