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