Man page - vcf-query(1)

Packages contains this manual

Package:  vcftools
apt-get install vcftools

Manuals in package:
• 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)
Documentations in package:
• vcftools

Manual

VCF-QUERY

NAME
SYNOPSIS
OPTIONS
EXAMPLES

---

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’

---