Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Multi-allelic sites in VQSR
I was wondering how GATK VQSR deals with multi-allelic sites.
I already know that -
i) VQSR treats them same way as bi-allelic sites (https://gatkforums.broadinstitute.org/gatk/discussion/7754/how-vqsr-deals-with-multiallelic-snps-and-indel)
ii) Split multi-allelic sites before VQSR (https://gatkforums.broadinstitute.org/gatk/discussion/23559/split-multiallelic-variants-before-vqsr-and-cnnscorevariants-gatk-team-opinion).
This mainly informs about mixed (SNP + INDEL) multi-allelic sites.
1. Do you recommend split multi-allelic SNPs before VQSR? Will it be biased since site-level information/annotation would be multiple counted. I got different results in split and NOT split (performed relatively better)
2. If we don't split multi-allelic SNP sites then how Ti/Tv ratio is calculated.
chr1 123 A T,G chr2 234 C *,A,T
In these above cases, which allele(s) is taken to calculate the Ti/Tv ratio in the tranche file. If VQSR takes the first allele then what to expect in 2nd case, where a star allele is at first position Or it is better to remove star alleles before VQSR?