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.