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Store per-site total depth of coverage #9

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akotlar opened this issue Aug 1, 2018 · 0 comments

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akotlar commented Aug 1, 2018 •

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Requested in https://github.com/akotlar/bystro/issues/35

Goal is to simply read the DP field in INFO if provided. Easiest way to check if present is to read VCF header.

Decision: do we want to create a dp column even if no dp is provided?

Progress

Create function to read vcf header, looking for INFO=<ID=DP,Number=1. Q: Is this sufficient or are there many permutations of this?
Figure out whether multi allelic and MNP sites give multiple depths of coverage.
Code implementation that handles multi-allelics and MNPs

akotlar mentioned this issue

Depth of coverage bystrogenomics/bystro#35

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