VCF-ANNOTATE(1)

💖 VCF-ANNOTATE 💖

okay bestie, so like — this is the manual page for vcf-annotate, one of the User Commands, and it is literally about to become your new hyperfixation. sit down, grab a strawberry 🍓, and let's get into it.

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✨ NAME ✨

vcf-annotate — annotate a VCF file, add filters or custom annotations. it's giving glow-up for your variants 💅

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🌈 SYNOPSIS 🌈

cat in.vcf | vcf-annotate [OPTIONS] > out.vcf

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🦋 DESCRIPTION 🦋

About: it annotates a VCF file, adding filters or custom annotations. it requires a tabix indexed file with annotations — no index, no service, periodt.

Currently it annotates only the INFO column, but bestie it will be extended on demand. so like, if you need more, ask, and it shall be done 🙈

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👑 OPTIONS 👑

• -a, --annotations <file.gz> — the tabix indexed file that holds all the annotations. the format is CHR\tFROM[\tTO][\tVALUE]+. yes that's a real format, yes the backslashes are doing something, iykyk.
• -c, --columns <list> — the list of columns in the annotation file, like for real for real. e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. that little dash in there? that's saying "ignore the third column, she's not invited 💀". and if TO is not present, it just assumes TO equals FROM. chill of it honestly.
• -d, --description <file|string> — header annotation, bestie. e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'. you can also read the descriptions from a file, one annotation per line. options on options, we love to see it 🫶
• -f, --filter <list> — apply filters. the list goes in this format: flt1=value/flt2/flt3=value/etc.
• -h, -?, --help — this help message. hi 👋

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🎀 Filters 🎀

• + — apply all filters with default values. and yes it can be overridden, see the example below, don't worry I got you ✨
• -X — exclude the filter X. bye girl 👋 not you.

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1. 1, StrandBias — FLOAT — min P-value for strand bias (given PV4) [0.0001]
2. 2, BaseQualBias — FLOAT — min P-value for baseQ bias [1e-100]
3. 3, MapQualBias — FLOAT — min P-value for mapQ bias [0]
4. 4, EndDistBias — FLOAT — min P-value for end distance bias [0.0001]
5. a, MinAB — INT — minimum number of alternate bases [2]
6. c, SnpCluster — INT1,INT2 — filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases [[] — yeah, empty, no default, she's a blank slate 🧚]
7. D, MaxDP — INT — maximum read depth [10000000]
8. d, MinDP — INT — minimum read depth [2]
9. q, MinMQ — INT — minimum RMS mapping quality for SNPs [10]
10. Q, Qual — INT — minimum value of the QUAL field [10]
11. r, RefN — reference base is N [[] — again, no default, just vibes]
12. W, GapWin — INT — window size for filtering adjacent gaps [10]
13. w, SnpGap — INT — SNP within INT bp around a gap to be filtered [10]

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🌸 Example 🌸

here's the moment you've been waiting for, the example, the main character of this manpage:

zcat in.vcf.gz | vcf-annotate -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz
zcat in.vcf.gz | vcf-annotate -f +/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz

see that +/-a/c=3,10/q=3/d=5/-D? that's the override moment — + grabs all the filters, -a and -D kick out MinAB and MaxDP, and the rest get their custom values. she ate 🔥

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🍓 Where descriptions.txt contains:

key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name'
key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'

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💀 real talk though bestie: the annotation file must be tabix indexed or nothing works. that's not a vibe, that's a requirement.

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and that's the whole page, no cap. this manual is for vcf-annotate version 0.1.5, dated July 2011 — an absolute icon, an elder, a legend, and honestly? still slaying. go annotate something, you're gonna do great 🫶✨💖