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PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool
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Capture homozygous reference INDELs based on individual positions #182

Open BinglanLi opened 4 months ago

BinglanLi commented 4 months ago

We have received a request to improve how the VCF Preprocessor recognizes homozygous reference INDELs. See the description and discussion of the issue on a previous issue thread. The idea is that if all genomic positions for an INDEL variant are homozygous reference, then, this should be sufficient evidence to deduce that no genetic variation is observed and the individual should be represented as homozygous reference for the INDEL variant.

This improvement has more use for basepair-resolution gVCF files that are generated by the GATK HaplotypeCaller.

This feature is currently waiting on the bcftools team to address a bug in merging INDEL records, bcftools issue #2163.

We will continue developing the feature once the bug is resolved.

moe1619 commented 1 month ago

bcftools seems to have closed this issue https://github.com/samtools/bcftools/issues/2163

BinglanLi commented 1 month ago

I appreciate the reminder. The issue is closed but the problem still lingers, e.g., case 2 in the https://github.com/samtools/bcftools/issues/2163. If the recommendation from the bcftools team works for your data, that is great. On the other hand, this feature is still under development and testing.