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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

Multi-mapping reads causing errors in Mutect2 for RNAseq?



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    Bhanu Gandham

    Hi ,

    The GATK support team is focused on resolving errors and abnormal results from GATK tools. For all other questions, such as this one which is about understanding how the tool works, we are building a backlog to work through when we have the capacity.

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    David Benjamin

    This error can only happen when three or more reads have the same name.  It can occur when a supplementary alignment falls very close to the primary alignment read pair, but if your samtools stats are to be believed it's happening for some other reason.  We have often seen pipelines where it happens a handful of times in a bam.

    Mutect2 now handles this by randomly choosing two reads rather than failing, but we haven't had a release since this change was merged.  There should be a GATK minor release next week.  Once that release comes out I would strongly recommend turning off the `independent-mates` argument, which tells Mutect2 to be ignorant of read-pairing during genotyping.

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    Good to hear, thank you!

    I will try removing all multiple-mapping reads too, see if that solves the issue.

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