ReferenceConfidenceVariantContextMerger.merge() should use remapped alleles when genotyping #8317
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droazen
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May 12, 2023
…tMerger to perform allele remapping prior to genotyping This is intended to tide the GVS team over until #8317 is fixed.
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See #8318 for an implementation of the desired behavior. |
mcovarr
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May 12, 2023
…tMerger to perform allele remapping prior to genotyping This is intended to tide the GVS team over until #8317 is fixed.
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Currently
ReferenceConfidenceVariantContextMerger.merge()does not pass in the remapped alleles toGATKVariantContextUtils.makeGenotypeCall()for theoriginalGTargument, which seems problematic and could cause the code to incorrectly fall back on reference calls in some cases. The GVS team has found it necessary to use the remapped alleles when genotyping in order to get correct genotypes out of the merge -- we should make this behavior the default.Currently, making it the default causes failures in the tests for the
--include-non-variant-sitesargument inGenotypeGVCFs(see #8288 (comment)). This appears related to the current implementation incorrectly calculating the reference allele when we are at some non-zero offset from the start of a GVCF reference block.The text was updated successfully, but these errors were encountered: