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GATKProtectedVariantContextUtils.chooseAlleleForRead mishandles read ends #5325

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davidbenjamin opened this issue Oct 18, 2018 · 1 comment
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GATKProtectedVariantContextUtils.chooseAlleleForRead mishandles read ends #5325

davidbenjamin opened this issue Oct 18, 2018 · 1 comment
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Mutect validation

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Reads that match the reference allele but end inside the VariantContext are sometimes counted as alt.
@davidbenjamin davidbenjamin self-assigned this Oct 18, 2018
@davidbenjamin davidbenjamin mentioned this issue Oct 18, 2018
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#5359 addresses the issue better.

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fixed edge case where SomaticValidator counts reads ending inside ref as alts broadinstitute/gatk
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