FastQTL(1)

💖 FastQTL 💖

okay so bestie, welcome to the FastQTL manual page — that's the General Commands Manual section 1 vibe, iykyk. she's a QTL mapper, she's iconic, she's about to change your whole genomics career. let's get into it 🧚✨

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✨ NAME ✨

FastQTL — Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes 🧬💅

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🌸 SYNOPSIS 🌸

fastQTL [options]

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🦋 DESCRIPTION 🦋

okay so here's the tea 🍓 — the whole goal of FastQTL is to identify single-nucleotide polymorphisms (SNPs) that are significantly associated with various molecular phenotypes (like, expression of known genes, cytosine methylation levels, etc. — she's versatile, she contains multitudes 💜).

She performs scans for all possible phenotype-variant pairs in cis — meaning variants located within a specific window around a phenotype. No cap, she does all of them.

And then — the main character moment — FastQTL implements a new permutation scheme (Beta approximation) to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels. she ate that 🔥

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👑 OPTIONS 👑

💫 Basic options

• --help — prints help about options. the "bestie what do I do" button 🫶
• --silent — silent mode on terminal. she's not talking rn 🙈
• --seed arg (=1459232241) — random number generator seed. super useful when you want to replicate runs of the software — same seed, same results, periodt. the default is literally 1459232241.

📁 Input and Output files options

• -L, --log — screen output gets copied into this file. receipts, basically 💅
• -V, --vcf — genotypes in VCF format.
• -B, --bed — phenotypes in BED format.
• -C, --cov — covariates in TXT format.
• -G, --grp — phenotype groups in TXT format.
• -O, --out — output file. the moment of truth ✨

🚫 Exclusion and Inclusion files options

• --exclude-samples — list of samples to exclude. bye girl 👋
• --include-samples — list of samples to include. come thru 🎀
• --exclude-sites — list of sites to exclude.
• --include-sites — list of sites to include.
• --exclude-phenotypes — list of phenotypes to exclude.
• --include-phenotypes — list of phenotypes to include.
• --exclude-covariates — list of covariates to exclude.
• --include-covariates — list of covariates to include.

⚙️ Parameters

• --normal — performs quantile normalization on the phenotype quantifications to make them normally distributed. implemented as the rntransform function of the GenABEL package. she's getting her life together 🌈
• -W, --window — cis-window size. the default value is 1Mb (1e6). what that means: all variants within 1e6 bp of the phenotype location (e.g. TSS) get analyzed. so like, a whole neighborhood gets a vibe check.
• -T, --threshold — filters out all phenotype-variant pairs with a p-value above the specified threshold in the output of a nominal pass. no mediocre p-values allowed 💀

🎭 Modes

• -P, --permute — permutation pass to calculate corrected p-values for molecular phenotypes.
• --psequence — permutation sequence.
• --map — maps best QTL candidates per molecular phenotype. finding the main character of each phenotype 👑
• --map-full — scans the full cis-window to discover independent signals. she's thorough ✨
• --interaction — tests for interactions with the variable specified in file.

🏃♀️ Parallelization

• -K, --chunk — specify which chunk needs to be processed. divide and conquer, bestie.
• --commands — generates all commands. she's writing the to-do list for you 🫶
• -R, --region — region of interest.

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🌟 EXAMPLE 🌟

here's the iconic loop, in all her glory:

for c in $(seq 1 256); do
     fastQTL --vcf genotypes.vcf.gz
             --bed phenotypes.bed.gz
             --chunk $c 256
             --permute 1000
             --out results.$c.txt.gz
done
zcat results.*.txt.gz | gzip -c > fastqtl_expected_output.txt.gz

note: this is copied exactly as she appears in the original page — the line breaks inside the fastQTL invocation are how they're written there, so don't come for me 🙈

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🔗 SEE ALSO 🔗

• http://fastqtl.sourceforge.net/ — go say hi to her website bestie 🌐

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💜 AUTHOR 💜

FastQTL was written by Olivier Delaneau, Halit Ongen, Alfonso Buil and Manolis Dermitzakis. absolute legends, all four of them 🔥👑

This manual page was written by Dylan Aïssi <bob.dybian@gmail.com>, for the Debian project (but may be used by others). shoutout to Dylan for the lore drop 🎀

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okay and that's the whole page bestie!! this is version 2.184 from March 2016 — yeah she's a vintage icon and she still eats 💅✨ go run some cis-QTL scans, ily, bye!! 🌸🦋💖