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

Counld I use bam files from HISAT2 to call snp/indels?



  • Official comment
    Genevieve Brandt (she/her)

    Hi Qun,

    Yes, as long as the output from HISAT2 are valid BAM files. Our best practices recommendation uses BWA, but you should be able to use HISAT2 if you prefer it. If you run into issues when you try to use these BAM files, let us know and we can help troubleshoot.



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    Genevieve Brandt (she/her)

    Hi Qun,

    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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