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ReadPosRankSumTest with leading insertions #6294

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kachulis opened this issue Dec 2, 2019 · 1 comment · Fixed by #6485
Closed

ReadPosRankSumTest with leading insertions #6294

kachulis opened this issue Dec 2, 2019 · 1 comment · Fixed by #6485
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@kachulis
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kachulis commented Dec 2, 2019

For an insertion variant, if a read provides evidence for the variant through a leading insertion, the ReadPosRankSumTest will ignore that read in the calculation of the annotation. This is because ReadUtils.getReadCoordinateForReferenceCoordinate will return ReadUtils.CLIPPING_GOAL_NOT_REACHED in this case, which will cause the read to be skipped for the purposes of the annotation. As a result, a variant where all the evidence is from leading insertions will have no ReadPosRankSum annotation calculated, even though this annotation should in that case provide strong evidence of an artifact.

@davidbenjamin
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@kachulis i'm working on a related bug. It makes sense to bring this into that effort.

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