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oxfordmmm / gnomonicus

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
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fix: if a gvcf row has a COV field, don't use DP #78

Closed JeremyWesthead closed 2 months ago

JeremyWesthead commented 2 months ago

Sundial's final.full.vcf which is a proxy for clockwork's gvcf doesn't use the same fields. Gvcf lacks a COV field, instead using DP for this. Sundial, being more sane, uses DP to mean total depth and has a COV field already. Before this, sundial's DP field was overriding with COV, and pysam's parsing treated both as the first value (which didn't have expected values)

This didn't cause an error though as this is technically fine and a valid VCF. It did however cause issues around merged in rows with expected minor populations (which rely on the COV field to be found)

JeremyWesthead commented 2 months ago

It's actually just because I didn't git pull before branching - latest release is 2.6.7 so this should be right