GTF file compressed indexing for IGV compatibility

index-gtf.sh

#!/bin/bash                                                                                                                                    

if [ "$#" -ne 1 ]; then
  echo -e "Incorrect number of parameters! Usage:\n    index-gtf.sh <file.gtf(.gz)>" >&2
  exit 1
fi

gtf="$1"

if [[ $gtf =~ \.gz$ ]]; then
  output=${gtf%.gtf.gz}.sorted.gtf.gz
  zcat $gtf | awk '!( $0 ~ /^#/ )' | sort --parallel=4 -S4G -k1,1 -k4,4n | bgzip -c > $output
else
  output=${gtf%.gtf}.sorted.gtf.gz
  cat $gtf | awk '!( $0 ~ /^#/ )' | sort --parallel=4 -S4G -k1,1 -k4,4n | bgzip -c > $output
fi
tabix $output