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Variant annotations at multialleleic sites

I was wondering how variant annotations are calculated for sites with multiple alternate alleles. Annotations like AC and AF have an entry for each allele, but annotations like QD and SOR only have one entry for the site regardless of number of alleles.

I'm assuming QD, SOR, etc. are calculated using all alt reads without distinguishing the different alleles, but couldn't find any information on this exact question.

I am wondering if its possible that a multiallelic site can PASS VQSR/hardfiltering based on site level quality annotations but still contain low quality alt alleles. Essentially, can low quality alternate alleles "tag along" with a high quality alternate allele at a multiallelic site.

A small example from my VCF:

1 9078420 . C T,CA

Best Answers


  • buckleya2buckleya2 Member

    Thanks! In order to use allele-specific VQSR would I have to re-generate my gVCFs? I saw this in the documentation of VariantRecalibrator -AS

    "The input VCF must have been produced using allele-specific annotations in HaplotypeCaller."

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