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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'