bankhead3 / sv-merge

sv-merge

A python tool to perform sample-specific merging of SV vcf files by combining events with matching breakends given a slack parameter (e.g. 200bp). Creates combined .txt and .vcf files.

Requirements

• python3
• python packages: pandas, pyranges, PyVCF

Usage

• download this github repo
• to run: sv-merge/sv-merge.py --vcfs sample.manta.vcf,sample.svaba.vcf,sample.gridds.vcf --sample-name sample
• creates 3 types of files:
  1. caller.txt files: tab-delimited text file with all standard chromosome calls
  2. comparison.txt files: file containing matched calls between different callers
  3. sv-merge.txt files: file containing the merged calls where calls by two or more callers have been combined

Assumptions and caveats to be aware of...

• Currently: manta,svaba,gridss calls supported
• Non-standard chromosome (e.g. alt, random, Unknown) are excluded
• Merged events require that both breakends match within 200bp
• manta/gridss del,ins,tandem dup events not merged due to missing alt orientation information. All events are parsed and written to caller.txt files.
• If something doesn't work the way it should - let's discuss and fix