vcf-subset (1)

vcf-subset [OPTIONS] in.vcf.gz > out.vcf

-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.

• cat in.vcf | vcf-subset -r -t indels -e -c SAMPLE1 > out.vcf