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

Germline mutations in Mutect2 vs HaplotypeCaller



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    Bhanu Gandham

    Hi ,

    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.

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    Hi vctrymao

    Somatic variant callers surely can find germline mutations, there no out-of-the-box way to distinguish germline and somatic mutations on the level of calling. However, there are multiple approaches to distinguish the somatic and germline variants after genotype calling via comparison with common SNP and INDEL databases (e.g. dbSNP, Mills Gold, etc),  matched normal case (genotype calling performed on data obtained from healthy tissue of the same biological subject), etc. You can find additional information here and elsewhere googling "discrimination of somatic and germline mutations".

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