Man page - vcf-query(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-QUERY(1) | User Commands | VCF-QUERY(1) |
NAME
vcf-query - query VCF files
SYNOPSIS
query-vcf [OPTIONS] file.vcf.gz
OPTIONS
- -c, --columns <NA001,NA002,..>
- List of comma-separated column names.
- -f, --format <string>
- The default is '%CHROM:%POS\t%REF[\t%SAMPLE=%GT]\n'
- -l, --list-columns
- List columns.
- -r, --region chr:from-to
- Retrieve the region. (Runs tabix.)
- -h, -?, --help
- This help message.
EXAMPLES
- query-vcf file.vcf.gz 1:1000-2000 -c NA001,NA002,NA003 query-vcf file.vcf.gz -r 1:1000-2000 -f '%CHROM:%POS\t%REF[\t%SAMPLE:%*=,]\n' query-vcf file.vcf.gz -f '[%GT\t]%LINE\n' query-vcf file.vcf.gz -f '%CHROM\t%POS\t%INFO/DP\t%FILTER\n'
| July 2011 | vcf-query 0.1.5 |