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BAM header filtering #54

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yashpatel6 opened this issue Mar 1, 2024 · 0 comments
Open

BAM header filtering #54

yashpatel6 opened this issue Mar 1, 2024 · 0 comments

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@yashpatel6
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yashpatel6 commented Mar 1, 2024 •
edited

Update filtering of BAM header lines to exclude @PG from other samples.

Currently IndelRealignment gather the BAMs of all samples and then ApplyBQSR separates them into sample-specific BAMs. As a part of the separation, the header @PG lines should also be filtered to keep only the ones for the specific sample. The alignment lines are copied from all samples currently.
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