Man page - vcf-subset(1)
Packages contains this manual
- vcf-query(1)
- vcf-stats(1)
- vcf-to-tab(1)
- vcf-concat(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-phased-join(1)
- fill-aa(1)
- vcf-isec(1)
- vcf-consensus(1)
- vcf-tstv(1)
- vcf-merge(1)
- vcf-subset(1)
- vcf-contrast(1)
- vcf-fix-newlines(1)
- fill-an-ac(1)
- vcftools(1)
- vcf-validator(1)
- fill-fs(1)
- vcf-fix-ploidy(1)
- vcf-compare(1)
- fill-ref-md5(1)
- vcf-annotate(1)
- vcf-convert(1)
- vcf-shuffle-cols(1)
apt-get install vcftools
Manual
VCF-SUBSET
NAMESYNOPSIS
OPTIONS
EXAMPLES
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