change 0/0 GQ0 sites to no-calls #7190
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| @@ -365,7 +365,8 @@ private void processSampleRecordsForLocation(final long location, final Iterable | |||
| currentPositionHasVariant = true; | |||
| break; | |||
| case "0": // Non Variant Block with GQ < 10 | |||
| unmergedCalls.add(createRefSiteVariantContextWithGQ(sampleName, contig, currentPosition, refAllele, 0)); | |||
| // Reference calls with GQ 0 should be rendered as no-call (#271) | |||
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this will functionally include reference calls with GQ >0 but <10, right? that's intended?
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Right -- post reblocking there are only GQs in increments of 10 (ie 0, 10, 20...). So we are changing the GQ 0s to no calls here, even if that was a GQ2 pre reblocking
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There is no separate GQ here, for reference calls that is encoded in the state (pet)
RoriCremer
approved these changes
Apr 8, 2021
mmorgantaylor
approved these changes
Apr 8, 2021
This was referenced Mar 17, 2023
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Resolves https://github.com/broadinstitute/dsp-spec-ops/issues/271