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