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Reduce false negatives from mapping quality filter on long indels in Mutect2 #5497

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merged 1 commit into from Dec 7, 2018

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@davidbenjamin
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commented Dec 7, 2018

@takutosato Our sensitivity on long indels was getting hurt because in some bams they have very low mapping quality (their score is penalized for having an indel) even if they map uniquely. This fixes that.

@davidbenjamin davidbenjamin merged commit b710639 into master Dec 7, 2018
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@davidbenjamin davidbenjamin deleted the db_m2_map_qual branch Dec 7, 2018
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