gistfile1.txt

#!/bin/bash
# My first script

# make sure you always put $f in double quotes to avoid any nasty surprises i.e. "$f"
for f in ~/Desktop/dsg1_1000Genome/1000Genome_dsg1/1000Genome_dsg1/*
do
	echo "Processing $f file..."
	mv $f $f".vcf"
	bgzip $f".vcf"
	cat ~/Desktop/dsg1_1000Genome/arch_dsg1.fasta | perl vcf-consensus -s $f $f".vcf.gz" > $f".fa"
	# rm "$f"
done