Man page - vcf-subset(1)
Packages contas this manual
- vcf-subset(1)
- vcf-merge(1)
- vcf-compare(1)
- vcf-to-tab(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-contrast(1)
- vcf-isec(1)
- vcf-validator(1)
- fill-ref-md5(1)
- vcf-convert(1)
- vcf-annotate(1)
- vcf-concat(1)
- fill-an-ac(1)
- vcf-fix-newlines(1)
- vcf-query(1)
- vcf-stats(1)
- vcf-consensus(1)
- vcf-tstv(1)
- fill-aa(1)
- vcf-phased-join(1)
- fill-fs(1)
- vcf-shuffle-cols(1)
- vcftools(1)
- vcf-fix-ploidy(1)
Package: vcftools
apt-get install vcftools
apt-get install vcftools
Manuals in package:
Documentations in package:
Manual
| VCF-SUBSET(1) | User Commands | VCF-SUBSET(1) |
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
| July 2011 | vcf-subset 0.1.5 |