vcf-subset(1)
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
