IHS(1)

🌸 NAME 🌸

iHS — the integrated haplotype score calculator, aka your new fave VCF statistics bestie 💖

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✨ SYNOPSIS ✨

iHS –target 0,1,2,3,4,5,6,7 –file my.phased.vcf  –region chr1:1-1000 > STDOUT 2> STDERR

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🦋 DESCRIPTION 🦋

Okay so iHS calculates the integrated haplotype score, which measures the relative decay of extended haplotype homozygosity (EHH) for the reference and alternative alleles at a site. It's giving selection signal realness. See: voight et al. 2006, Spiech & Hernandez 2014. 📚

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💅 OPTIONS 💅

Our code is highly concordant with both implementations mentioned above. However, we do not set an upper limit to the allele frequency. No cap, literally.

iHS can be run without a genetic map, in which case the change in EHH is integrated over a constant. Human genetic maps for GRCh36 and GRCh37 (hg18 & hg19) can be found at: http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/ . iHS by default interpolates SNV positions to genetic position (you don't need a genetic position for every VCF entry in the map file). Slay. ✨

iHS analyses requires normalization by allele frequency. It is important that iHS is calculated over large regions so that the normalization does not down weight real signals. For genome-wide runs it is recommended to run slightly overlapping windows and throwing out values that fail integration (columns 7 & 8 in the output) and then removing duplicates by using the sort and uniq linux commands. Normalization of the output is as simple as running normalize-iHS.

iHS calculates the integrated ratio of haplotype decay between the reference and non-reference allele.

📊 Output 📊

It's 4 columns:

1. seqid
2. position
3. target allele frequency
4. integrated EHH (alternative)
5. integrated EHH (reference)
6. iHS ln(iEHHalt/iEHHref)
7. != 0 integration failure
8. != 0 integration failure

bestie the header says 4 and the list says 8, and we are simply not going to fight about it. moving on 💀

🎀 Params 🎀

• required: t,target <STRING> — A zero base comma separated list of target individuals corresponding to VCF columns
• required: r,region <STRING> — A tabix compliant genomic range format: "seqid:start-end" or "seqid"
• required: f,file <STRING> — Proper formatted and phased VCF.
• required: y,type <STRING> — Genotype likelihood format: GT,PL,GL,GP
• optional: a,af <DOUBLE> — Alternative alleles with frquences less than [0.05] are skipped.
• optional: x,threads <INT> — Number of CPUS [1].
• recommended: g,gen <STRING> — A PLINK formatted map file.

Type: statistics

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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 one came to you from iHS (vcflib), no cap, mwah 💖