May I know how VQSR deals with multiallelic SNPs and indels? How to classify them as pass or fail?
Regarding this situation of multiallelic sites, I also have one question.
I split multiallelic sites in my VCF using bcftools, but when I try to use GATK tool Variant Filtration, something happens when it finds repeated positions (first and second alternative allele) and stops reporting a bug.
Do you know why this happen? How can I prevent this?