tools/etc/vcf_downgrade.sh

   1 # If you are trying to view VCF 4.2 files in IGV - you may run into issues. This function might help you.
   2 # This script will:
   3 # 1. Rename the file as version 4.1
   4 # 2. Replace parentheses in the INFO lines (IGV doesn't like these!)
   5
   6 function vcf_downgrade() {
   7   outfile=${1/.bcf/}
   8   outfile=${outfile/.gz/}
   9   outfile=${outfile/.vcf/}
  10   bcftools view --max-alleles 2 -O v $1 | \
  11   sed "s/##fileformat=VCFv4.2/##fileformat=VCFv4.1/" | \
  12   sed "s/(//" | \
  13   sed "s/)//" | \
  14   sed "s/,Version=\"3\">/>/" | \
  15   bcftools view -O z > ${outfile}.dg.vcf.gz
  16   tabix ${outfile}.dg.vcf.gz
  17 }
  18