SHAPEIT4(1)

💖 SHAPEIT4 💖

okay so bestie, welcome to the SHAPEIT4(1) page — yeah it's a "General Commands Manual" page, but honestly? it's giving main character energy and we're gonna read it together. grab a snack 🍓

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✨ NAME ✨

shapeit4 — fast and accurate method for estimation of haplotypes (phasing)

like. it phases. it's fast. it's accurate. periodt.

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🌈 SYNOPSIS 🌈

shapeit4 [options]

that's it, that's the whole vibe check. you just run it with options and let it cook 💅

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🦋 DESCRIPTION 🦋

Segmented HAPlotype Estimation and Imputation Tools version 4 — aka SHAPEIT4, iykyk.

so SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and sequencing data. no cap.

it includes a Positional Burrow Wheeler Transform (PBWT) based approach to quickly select a small set of informative conditioning haplotypes to be used when updating the phase of an individual. literally so smart of it.

it accounts for sets of pre-phased genotypes (i.e. haplotype scaffold). and bestie, the scaffold can be derived either from family data or large reference panels — your choice, your era 💜

it reads and writes files using HTSlib for better I/O performance in either VCF or BCF formats. the genotype graph and HMM routines have been re-implemented for better hardware usage and performance. she got a glow-up fr fr ✨

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👑 OPTIONS 👑

🎀 Basic options

• --help — Produce help message. the "hi bestie what do you need" flag 🫶
• --seed arg (=15052011) — Seed of the random number generator. same seed, same results, that's the rule 🌸
• -T, --thread arg (=1) — Number of thread used. give her more threads, she'll go faster 🔥

🧚 Input files

• -I, --input arg — Genotypes to be phased in VCF/BCF format. your raw material, bestie
• -H, --reference arg — Reference panel of haplotypes in VCF/BCF format. the iconic elders we look up to 👑
• -S, --scaffold arg — Scaffold of haplotypes in VCF/BCF format. the structure holding it all together 💅
• -M, --map arg — Genetic map. the map. of genetics.
• -R, --region arg — Target region. zoom in on where you're working 📍
• --use-PS arg — Informs phasing using PS field from read based phasing. the PS field said "let me help" and honestly? we let it

🎲 MCMC parameters

• --mcmc-iterations arg (=5b,1p,1b,1p,1b,1p,5m) — Iteration scheme of the MCMC. that default string is a whole choreography, not me reading it like a dance routine 😭
• --mcmc-prune arg (=0.999) — Pruning threshold. she's pruning, she's selective, we love that for her 🌿
• --mcmc-store-K arg — Store K sizes in last iterations. keep the receipts from the final rounds 🧾

🌸 PBWT parameters

• --pbwt-disable-init — Do not initialise haplotypes by PBWT (rephase input haplotype data). turning off the init and rephasing the input haplotype data instead 🙈
• --pbwt-modulo arg (=8) — Storage frequency of PBWT indexes in variant numbers (i.e. 16 means storage every 16 variants). so like, 16 = every 16 variants. cute little storage schedule ✨
• --pbwt-depth arg (=4) — Depth of PBWT indexes to condition on. how deep we're conditioning, no pun intended (pun fully intended)

💜 HMM parameters

• -W, --window arg (=2000000) — Minimal size of the phasing window. the minimal size, so it can be bigger, she just won't go smaller 🪟
• --effective-size arg (=15000) — Effective size of the population. 15000 of them. iconic crowd

💾 Output files

• -O, --output arg — Phased haplotypes in VCF/BCF format. the final look, the reveal, the slay 💖
• --log arg — Log file. so you can read back what happened like a diary entry 📓

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🔗 SEE ALSO 🔗

• https://odelaneau.github.io/shapeit4/

go read the docs bestie, they're right there 🫶

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🖊️ AUTHOR 🖊️

SHAPEIT4 was written by Olivier Delaneau. thank you Olivier, you ate 💅✨

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lowkey reminder: this page is from December 2018, and it's the SHAPEIT4(1) manual page from the General Commands Manual section — so if you're reading this in the future, just know she's been iconic since 2018 💖🦋🎀 ok bye ily, go phase something 🧬🌈