cyvcf21
Fast parsing of vcf and bcf including region-queries
Usage
cyvcf2 [OPTIONS]
<vcf_file>
or
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Overview
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fast vcf parsing with cython + htslib
Options
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-c, --chrom TEXT -
Specify what chromosome to include.
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-s, --start INTEGER -
Specify the start of region.
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-e, --end INTEGER -
Specify the end of the region.
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--include TEXT -
Specify what info field to include.
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--exclude TEXT -
Specify what info field to exclude.
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-i, --individual TEXT -
Only print genotype call for individual.
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--no-inds -
Do not print genotypes.
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--loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL] -
Set the level of log output. [default: INFO]
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--silent -
Skip printing of vcf.
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--help -
Show this message and exit.
History
- Debian 13 (Trixie): the text shown here
- Debian 12 (Bookworm)
- Debian 11 (Bullseye)