VCFFILTER(1)

✨ VCFFILTER ✨

okay bestie, welcome to the vcffilter(1) era 💅 this is the manual page for vcffilter, and she is that girl when it comes to slicing and dicing VCF files. let's get into it 🧚

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🌸 NAME 🌸

vcffilter — the VCF filter of your dreams 💖

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🎀 SYNOPSIS 🎀

vcffilter options

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🦋 DESCRIPTION 🦋

VCF filter the specified vcf file using the set of filters. that's it, that's the whole vibe. you bring the filters, she brings the filtering. periodt ✨

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💅 OPTIONS 💅

okay so here's the full menu, no cap, every single one:

• -f, --info-filter — specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter 🔥
• -g, --genotype-filter — specifies a filter to apply to the genotype fields of records
• -k, --keep-info — used in conjunction with -g, keeps variant info, but removes genotype 👑
• -s, --filter-sites — filter entire records, not just alleles
• -t, --tag-pass — tag vcf records as positively filtered with this tag, print all records ✅
• -F, --tag-fail — tag vcf records as negatively filtered with this tag, print all records 💀
• -A, --append-filter — append the existing filter tag, don't just replace it
• -a, --allele-tag — apply -t on a per-allele basis. adds or sets the corresponding INFO field tag
• -v, --invert — inverts the filter, e.g. grep -v 🙈
• -o, --or — use logical OR instead of AND to combine filters
• -r, --region — specify a region on which to target the filtering, requires a BGZF compressed file which has been indexed with tabix. any number of regions may be specified. 📍

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✨ how the filters actually work ✨

Filter the specified vcf file using the set of filters.

Filters are specified in the form "<ID> <operator> <value>:

-f "DP > 10"  # for info fields
-g "GT = 1|1" # for genotype fields
-f "CpG"  # for 'flag' fields

Operators can be any of: =, !, <, >, |, &

Any number of filters may be specified. They are combined via logical AND unless --or is specified on the command line. Obtain logical negation through the use of parentheses, e.g. "! ( DP = 10 )" 🫶

For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields. iconic honestly ⭐

type: filter

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🌈 EXIT VALUES 🌈

• 0 — Success 🎉
• not 0 — Failure 😭

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👑 SEE ALSO 👑

• vcflib(1)

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💜 OTHER 💜

LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

AUTHORS

Erik Garrison and vcflib contributors.

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and that's the whole page, bestie 🫶 this was vcffilter from the vcflib family, page 1, brought to you by Erik Garrison, Pjotr Prins and the vcflib contributors. go filter something gorgeous 💖✨🌸