rustvcf

Purpose

This is a rust CLI tool intended to remove INFO annotations from VCF files and replace them with ".". The objective is to beat awk in a current project which takes ~25mins per sample.

Performance

From the 1000 genomes project

File	Size	Time
ALL.chr14.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz	163MB	~40s
ALL.chr22.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz	383MB	~116s

Install

To install make sure you have cargo v1.87 at least. To produce the executable run: cargo build --release

Usage

Compile

cargo build --release

For deannotation:

./target/release/rustvcf -t deannotate -i <path/to/input.vcf.gz> -o <path/to/output.vcf.gz>

For validation of the deannotated file (experimental/slow):

./target/release/rustvcf -t validate -i <path/to/deannotated_vcf.gz> -o None