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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.
The text was updated successfully, but these errors were encountered:
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 returnReadUtils.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.The text was updated successfully, but these errors were encountered: