LR Annotation
This repository contains code for processing cohorts sequenced with long-read genomic sequencing methods - from variant calling and callset integration, all the way through to phasing and annotation. The pipeline was run on two cohorts as part of its initial release - a combined set of 292 samples from the HPRC & HGSVC consortia and 1027 samples from Phase 1 of the All of Us initiative.
The pipeline covers three broad stages.
- Callset Generation: Per-sample variant calls from
This is a companion discussion topic for the original entry at github.com/talkowski-lab/lr-pipeline/ConcatenateMosDepth