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

Strange differences in detected variants called by mutect2 --dont-use-soft-clipped-bases true vs false


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    David Benjamin

    Jana Marie Schwarz turning off soft-clipped bases is usually not the right thing to do.  It takes information away from Mutect2, which as you have seen can change calls in both directions.

    I acknowledge that you want to disable soft-clips because they appear to be causing a false positive.  Perhaps they are -- Mutect2 is far from perfect.  However, very often soft clips are the only evidence for real indels.  To see what Mutect2's local assembly engine was "thinking", turn on the --bamout bamout.bam option and then view bamout.bam in IGV.

    The only circumstance in which I would always recommend discarding soft clips is when somewhere upstream in your pipeline things that should have been marked as hard clips were instead soft-clipped.  A soft-clipped base means something of biological origin for which the aligner simply couldn't assign a location.  Given infinite computing resources, aligners would search for large indels and there would be no such thing as soft clips.

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