danwiththeplan

#!/bin/bash
# script to convert .vcf file to .gff3 format

#set variables that do not vary across detected polymorphisms: name of the program used, and name of the reference sequence

software_type=$(cat $1| grep "##source="|cut -b 10-)
reference_sequence=$(cat $1| grep "##reference"|cut -b 13-)

#remove comment lines in .vcf file and pipe to a while loop