vcf-subset1
Create subset of vcf file
Usage
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-tindels-e-cSAMPLE1 > out.vcf
Releases
Unchanged in 7 releases since Debian 7 (Wheezy).