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 %REF[ %SAMPLE=%GT]
'
-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 %REF[ %SAMPLE:%*=,]
'
query-vcf file.vcf.gz -f '[%GT ]%LINE
' query-vcf file.vcf.gz -f '%CHROM %POS %INFO/DP %FILTER
'
vcf-query 0.1.5 July 2011 VCF-QUERY(1)
