Modify_gff_coordinates.sh

#!/bin/bash
#Author: Andrew Nelson andrewnelson@email.arizona.edu
#A bash script to add base pairs to the start and stop coordinates of a genome annotation file (GFF/GFF3/GTF) 
while getopts ":g:v:d:" opt; do
  case $opt in
    g)
      gfftomodify=$OPTARG #File to be modified
    ;;
    d)
      delimiter=$OPTARG #The label provided by the GTF/GFF file denoting the gene or CDS in which you are interested. For instance, most annotation files use gene, but some use Gene or CDS or mRNA.
    ;;
    v)
      basepairtomodify=$OPTARG #This is the number of base pairs that you want to add to the 5' and 3' of your gene. Both negative and positive values can be used here.
    ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      exit 1
      ;;
    :)
      echo "Option -$OPTARG requires an argument." >&2
      exit 1
      ;;
  esac
done
grep -v "#" $gfftomodify |grep -i "$delimiter	" |awk -v num="$basepairtomodify" '{OFS="\t"} {$4-=num}1' |awk -v num="$basepairtomodify" '{OFS="\t"} {$5+=num}1' >$gfftomodify.modified.gff