Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Is it better to 'CollectAllelicCounts' using bam files local assembled by Haplotypecaller or Mutect2?

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    Genevieve Brandt (she/her)

    Hi WangZiwei,

    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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    Samuel Lee

    Hi WangZiwei,

     

    I don't think using the bam outs from HC/M2 would be necessary. It's unlikely that the pileup counts would be affected in a way that the ModelSegments noise model could not handle.

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