vcf-subset - 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