vcf-subset(1) create subset of VCF file


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