NAME
cyvcf2 - fast parsing of VCF and BCF including region-queries
SYNOPSIS
cyvcf2 [OPTIONS] <vcf_file> or -
DESCRIPTION
-
fast vcf parsing with cython + htslib
OPTIONS
- -c, --chrom TEXT
-
Specify what chromosome to include.
- -s, --start INTEGER
-
Specify the start of region.
- -e, --end INTEGER
-
Specify the end of the region.
- --include TEXT
-
Specify what info field to include.
- --exclude TEXT
-
Specify what info field to exclude.
- -i, --individual TEXT
-
Only print genotype call for individual.
- --no-inds
-
Do not print genotypes.
- --loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]
-
Set the level of log output. [default: INFO]
- --silent
-
Skip printing of vcf.
- --help
-
Show this message and exit.