fas-to-vcf

Description

This is a Bash script to batch convert FAS files to VCF files using bwa, samtools, and bcftools

Requirements

samtools 1.9

bcftools 1.9

bwa 0.7.12

Input

1 reference file, 1 case-sensitive format of sequence files, up to 7 sequence id's

Sample Command

bash fas-to-vcf.sh ref.fasta fastq ERR221622 ERR221661 ERR221662 ERR221663

Output

up to 7 VCF files (and associated pre-cursor files used to generate the VCF file)

Folder Setup

Tree (Before):

Tree (After):