nate-d-olson/defrabb

Development Environment For Assembly Based Benchmarks

Development Framework for Assembly-Based Benchmarks (DeFrABB)

The GIAB benchmark set development framework is a snakemake bioinformatic pipeline for the development of transparent and reproducible genome assembly-based small and structural variant benchmark sets.

The defrabb code-base is now available at https://github.com/usnistgov/defrabb. This repo is now archived and read-only.

defrabb's Issues

Dipcall vcf

Hi @nate-d-olson

How do you post-process the dipcall vcf? The only way to make it work with hap.py is to use the old artifact code you mention

gunzip -c {input} |\
sed 's/1|\./1|1/' |\
grep -v 'HET\|GAP1\|DIP' |\
bgzip -c 1> {output} 2> {log}

Is there a better way?