vcf-query(1)
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'
