Provided by: vcftools_0.1.11+dfsg-1_amd64
NAME
vcf-subset - create subset of VCF file
SYNOPSIS
vcf-subset [OPTIONS] in.vcf.gz > out.vcf
OPTIONS
-c, --columns <string> File or comma-separated list of columns to keep in the vcf file. If file, one column per row -e, --exclude-ref Exclude rows not containing variants. -p, --private Print only rows where only the subset columns carry an alternate allele. -r, --replace-with-ref Replace the excluded types with reference allele instead of dot. -t, --type <list> Comma-separated list of variant types to include: SNPs,indels. -u, --keep-uncalled Do not exclude rows without calls. -h, -?, --help This help message.
EXAMPLES
cat in.vcf | vcf-subset -r -t indels -e -c SAMPLE1 > out.vcf