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

Perform realignment around indels before detecting MSI on BAM files?



  • Official comment
    Genevieve Brandt (she/her)

    Hi David Lord,

    Thanks for your question. We aren't able to provide a definitive answer because this isn't quite in our scope

    We would recommend reaching out to the team that makes the MSI-analysis software to see what pre-processing steps they recommend. If they recommend indel realignment, you could go back to GATK3 and use the indel realignment tool in that package. Like you said, the reason we don't have a stand alone tool for indel realignment is because our variant callers perform indel realignment within the tools.



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    Pamela Bretscher

    Hi David Lord,

    I am going to move your post into our Community Discussions -> General Discussion topic, as the somatic topic is for reporting bugs and issues with GATK.
    You can read more about our forum guidelines and the topics here: Forum Guidelines.


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