VEP for loop bash file

#!/bin/bash

echo 'This is to run VEP version 93 cache 94 GRCh37'

# Program path

VEP_path=/mnt/bigHDD/resource/ref_and_tools/tools/ensembl-vep/vep

dir_cache=/mnt/bigHDD/resource/ref_and_tools/tools/ensembl-vep/caches/homo_sapiens_merged

fasta_file=/mnt/bigHDD/resource/ref_and_tools/reference/human/ensembl/GRCh37.75/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa

# Get current directory's VCF files

ls | grep .vcf > input_VCF.file.list.txt

echo 'Input VCF file list created (input_VCF.file.list.txt)'

# Create output directory

mkdir VEP_ver93_cache94_GRCh37_result

outdir='/VEP_ver93_cache94_GRCh37_result/'

echo 'Output direcory created (VEP_ver93_cache94_GRCh37_result)'

# Get current directory path and output directory

input_path=$(pwd)

output_path=$input_path$outdir

output_file='_VEP.ver93.cache94.grch37.txt'

# Conducting VEP programm

for x in $(cat input_VCF.file.list.txt)

do

echo $x

output_file_name=$output_path$x$output_file

$VEP_path --no_stats --offline --tab --verbose --protein --symbol --uniprot \

--canonical --sift b --polyphen b \

--cache --cache_version 94 --dir_cache $dir_cache \

-i $x \

-o $output_file_name \

--fasta $fasta_file

#echo $output_file_name

done