EAGLE(1)

💖 EAGLE(1) — the manual page, but make it cute 💖

okay bestie, so this is the general commands manual page for eagle, and I need you to know right now that this little binary is the moment. no cap. let's get into it ✨

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✨ NAME ✨

eagle — haplotype phasing within a genotyped cohort or using a phased reference panel 🦋

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🌸 SYNOPSIS 🌸

eagle [options]

that's it. that's the whole synopsis. she's simple, she's elegant, she's literally just vibes and flags 💅

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💫 DESCRIPTION 💫

so basically, Eagle estimates haplotype phase either within a genotyped cohort or using a phased reference panel. two paths, one icon 👑

the Eagle1 algorithm has a whole thing going on: it harnesses identity-by-descent among distant relatives — which, and this is the key part, is pervasive at very large sample sizes but rare among smaller numbers of samples — to rapidly call phase using a fast scoring approach. it's giving speed, it's giving efficiency, it's giving "we found our cousins and they're helping" 🫶

meanwhile the Eagle2 algorithm is the main character who does the deep work: it analyzes a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. she's thorough. she's modeling. she's not cutting corners 😭

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🎀 OPTIONS 🎀

here we go, the flag buffet. no skipping, we're reading all of them, that's the rule ✨

• -h, --help — print this help 💖
• --geneticMapFile arg — the HapMap genetic map that comes with the download: tables/genetic_map_hg##.txt.gz
• --outPrefix arg — prefix for output files
• --numThreads arg (=1) — number of computational threads (default is 1, so if you want her to multi-task you gotta say so)

🧬 Input options for phasing without a reference

no reference panel? no problem, she's got options:

• --bfile arg — prefix of PLINK .fam, .bim, .bed files
• --bfilegz arg — prefix of PLINK .fam.gz, .bim.gz, .bed.gz files
• --fam arg — PLINK .fam file (note: file names ending in .gz are auto-decompressed — she does it for you, no manual unzipping required 🧚)
• --bim arg — PLINK .bim file
• --bed arg — PLINK .bed file
• --vcf arg — [compressed] VCF/BCF file containing input genotypes
• --remove arg — file(s) listing individuals to ignore (no header; FID IID must be first two columns) — bye bestie 👋
• --exclude arg — file(s) listing SNPs to ignore (no header; SNP ID must be first column) — also bye 👋
• --maxMissingPerSnp arg (=0.1) — QC filter: max missing rate per SNP (default 0.1)
• --maxMissingPerIndiv arg (=0.1) — QC filter: max missing rate per person (default 0.1)

📚 Input/output options for phasing using a reference panel

now with a reference panel in the mix, things get fancy:

• --vcfRef arg — tabix-indexed [compressed] VCF/BCF file for reference haplotypes
• --vcfTarget arg — tabix-indexed [compressed] VCF/BCF file for target genotypes
• --vcfOutFormat arg (=z) — b|u|z|v: compressed BCF (b), uncomp BCF (u), compressed VCF (z), uncomp VCF (v) — default is z, the compressed VCF, classic 💅
• --noImpMissing — disable imputation of missing ./. target genotypes
• --allowRefAltSwap — allow swapping of REF/ALT in target vs. ref VCF

🗺️ Region selection options

pick your little window of the genome, bestie:

• --chrom arg (=0) — chromosome to analyze (if input has many) — default 0
• --bpStart arg (=0) — minimum base pair position to analyze — default 0
• --bpEnd arg (=1e9) — maximum base pair position to analyze — default 1e9, so basically the whole thing unless you say otherwise
• --bpFlanking arg (=0) — (ref-mode only) flanking region to use during phasing but discard in output — default 0

🧠 Algorithm options

the brainy section. the iykyk section. let's go:

• --Kpbwt arg (=10000) — number of conditioning haplotypes — default 10000
• --pbwtIters arg (=0) — number of PBWT phasing iterations (0=auto) — default 0
• --expectIBDcM arg (=2.0) — expected length of haplotype copying (cM) — default 2.0
• --histFactor arg (=0) — history length multiplier (0=auto) — default 0
• --genoErrProb arg (=0.003) — estimated genotype error probability — default 0.003
• --pbwtOnly — in non-ref mode, use only PBWT iters (automatic for sequence data)
• --v1 — use Eagle1 phasing algorithm (instead of default Eagle2 algorithm) — the throwback option, nostalgic fr fr

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🔍 SEE ALSO 🔍

go read more, she's online:

• https://data.broadinstitute.org/alkesgroup/Eagle/

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📜 COPYRIGHT 📜

Copyright © 2015-2016 Harvard University. Distributed under the GNU GPLv3+ open source license.

like, respect the license bestie, it's the law 🫶

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⚠️ heads up: everything above is the whole page, nothing skipped, nothing invented. all the defaults, all the flags, all the args and all the = signs are exactly where they should be 💖

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and that's the whole page, bestie!! ✨🦋💅 this is version 2.3, dated September 2016, from the General Commands Manual — she's been iconic since 2016 and she's still serving. periodt. 💜👑