QTLtools-gwas(1)

Okay bestie, this is the page for QTLtools-gwas(1) from the bioinformatics tools crew 🧚 and it's giving main character energy ✨

✨ NAME ✨

QTLtools gwas is for genome-wide association tests 💖

📜 SYNOPSIS

QTLtools gwas --vcf [in.vcf|in.vcf.gz|in.bcf|in.bed.gz] --bed
quantifications.bed.gz --out output.txt [OPTIONS]

🌸 DESCRIPTION

Okay so this mode runs a linear regression with every genotype vs. every phenotype. Every single pair, no skipping 💅

🎀 OPTIONS

• --vcf [in.vcf|in.bcf|in.vcf.gz|in.bed.gz] ... — Your genotypes go in VCF/BCF/BED format 🦋 The DS field in the genotype FORMAT of a variant (the dosage calculated from genotype probabilities, e.g. after imputation) is REQUIRED. REQUIRED.
• --bed quantifications.bed.gz ... — Molecular phenotype quantifications in BED format. REQUIRED 🍓
• --out filename.txt — The output file name. REQUIRED 💜
• --cov covariates.txt — Covariates you want to correct the phenotype data with 🫶
• --normal — Rank normal transform the phenotype data so each phenotype comes out normally distributed. RECOMMENDED 🌈

📊 OUTPUT FILE

Output file vibes: it's a space separated file with these columns 🎀

• 1 — the phenotype ID
• 2 — the variant's chromosome
• 3 — the variant's start position
• 3.1 — the variant's end position. Only printed if a BED file is supplied to --vcf 👀
• 4 — the variant's ID
• 5 — the p-value
• 6 — the correlation coefficient

🧚 EXAMPLE

• Run the association between all the variants and phenotypes, correcting the phenotypes with technical covariates and normal transforming them 🔥

QTLtools gwas --bed quantifications.bed.gz --vcf genotypes.bcf --cov covariates.txt --normal --out gwas_results.txt

🔗 SEE ALSO

• QTLtools(1)
• QTLtools website: https://qtltools.github.io/qtltools 🦋

🙈 BUGS

Versions up to and including 1.2 suffer from a bug in reading missing genotypes in VCF/BCF files, bestie. 😭 This bug affects variants with a DS field in their genotype's FORMAT and have a missing genotype (DS field is .) in one of the samples. When that happens, genotypes for all the samples are set to missing, which effectively removes this variant from the analyses 💀

Please submit bugs to https://github.com/qtltools/qtltools 🐛

📚 CITATION

Delaneau O., Ongen H., Brown A. A., et al. A complete tool set for molecular QTL discovery and analysis. Nat Commun 8, 15452 (2017). https://doi.org/10.1038/ncomms15452 💜

👑 AUTHORS

Olivier Delaneau (olivier.delaneau@gmail.com), Halit Ongen (halitongen@gmail.com) 🫶

Signing off with QTLtools-v1.3, last updated 06 May 2020, for QTLtools-gwas(1) 🌈✨