a wrapper script for vcf2hetfa,pl from the SGDP project

vcf2hetfa.sh

#!/bin/bash

## bash vcf2hetfa.sh input.vcf.gz

VCF=$1
OUT=$(basename -s .vcf.gz $VCF).hetfa.fa
TMP=${OUT}.tmp

rm $OUT # output build by appending, so remove old versions first

for chr in {1..22}
do
	echo ">"${chr} >> $OUT
	bcftools view -t $chr $VCF | perl vcf2hetfa.pl --fasta_sample_prefix $TMP
	fold $TMP >> $OUT
	echo "" >> $OUT
done

rm $TMP

vcf2hetfa.sh

A simple wrapper script for vcf2hetfa.pl from the Simons Genome Diversity Project (SGDP). Takes a path/to/file.vcf.gz as argument and produces file.hetfa.fa in current directory (the original script doesn't support stdout). I use symlinks to have input files at reasonable paths. 👍️

Possible improvements:

• Don't hardcode input format (.vcf.gz is what I need right now, and it is a reasonable default).
• xargs or GNU parallel version would be awesome, possibly followed by seqkit sort or some such, for faster throughput. 👈️