Cohort SV detection pipeline

Table of contents

  1. Overview
  2. WDL scripts
  3. Docker images


This repository contains pipeline scripts for structural variation detection in large cohorts. The pipeline is designed for Illumina paired-end whole genome sequencing data, preferably with at least 30x sequence coverage. Data inputs should be a set of sorted CRAM files, aligned with BWA-MEM.

This pipeline detects structural variation based

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