MTtoVCF
The MTtoVCF pipelines take a Hail matrix table, apply quality and cohort filters, annotate variants using the AoU Variant Annotation Table (VAT), and export a VCF.
The specific matrix table is referred to as the superset matrix table, consisting of 10,750 multiomic samples.
Workflows
1. FilterMT.wdl (primary workflow)
This is the main, all-in-one workflow. It filters the matrix table, annotates variants from the VAT Hail table, and exports a VCF — all in a single ste
This is a companion discussion topic for the original entry at github.com/AoU-Multiomics-Analysis/MTtoVCF/LoFCarrierTable