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

MUTECT2 bamout reports far more reads than original bam - reliable?


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    David Benjamin

    Jana Marie Schwarz The extra reads might be the artifical reads representing the locally-assembled haplotypes.  These will generally all have a uniform length that spans the entire assembly window, without ending in the middle like an actual read.  Also, they are marked with a fake read group tag -- I think it's "HP".  If you sort by read group in IGV this should stand out.

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