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AlleleCounter bahavior with soft-clipped reads #64

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DominikGlodzik opened this issue Jun 2, 2020 · 1 comment
Open

AlleleCounter bahavior with soft-clipped reads #64

DominikGlodzik opened this issue Jun 2, 2020 · 1 comment

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@DominikGlodzik
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Hello CancerIT Team,

could you confirm if soft-clipped reads are taken into account in pile-up calculations?

Best wishes
Dominik
@keiranmraine keiranmraine transferred this issue from cancerit/dockstore-cgpwgs Jun 2, 2020
@keiranmraine
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If a portion of a read is soft-clipped it cannot be considered during counting if that portion is overlapping as it is not considered mapped. @davidrajones may be able to provide further confirmation on this.

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@keiranmraine @DominikGlodzik