vcfverifier

Checks that a given VCF file matches a given assembly in FASTA format by checking that the REF column matches the FASTA file for each record in the FASTA file (case insensitive)

Install

First install rust, probably with rustup https://rustup.rs/

Then

cargo install vcfverifier

Usage

## Generated FASTA index (fai)
samtools faidx myfile.fa

## Run the verifier
vcfverifier --fasta myfile.fa --vcf myfile.vcf.gz

Allows plaintext, gzip, or bgzip vcf files as input to the --vcf flag

Approx speed

Processing chr1 (6.5M rows) of the 1000 genomes dataset takes ~24seconds

$ time vcfverifier --fasta hs37d5.fa --vcf ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
Lines processed: 6468347
No mismatching lines found
vcfverifier --fasta ~/Downloads/hs37d5.fa --vcf   24.07s user 0.26s system 99% cpu 24.330 total

Note

My first rust project!

Uses faimm to memory-map the indexed FASTA file, keeping memory usage low (the entire FASTA does not have to be loaded into memory and the VCF is read line by line) https://github.com/veldsla/faimm