This is the command vcf-query that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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'
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