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#!/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 |