QTLtools-correct(1)

✨ QTLtools-correct(1) ✨

Okay bestie, let's talk about QTLtools-correct(1) 💖 It's part of the Bioinformatics tools crew 🧚 and it is literally so good at correcting your data 💅

✨ NAME ✨

QTLtools correct — Corrects genotypes or phenotypes with the provided covariates 🎀

✨ SYNOPSIS ✨

QTLtools correct --vcf [in.vcf|in.vcf.gz|in.bcf] | --bed in.bed.gz --cov covariates.txt | --normal --out output.txt [OPTIONS]

✨ DESCRIPTION ✨

Okay so this mode corrects genotypes or phenotypes in VCF, BCF, or BED files 📂 using covariates you hand it, and/or rank normal transforms your data 🌈 Then it writes the new corrected values out to a file. The vibe is that it regresses out the covariates from your data and saves the residuals to a file. Main character energy 👑

✨ OPTIONS ✨

• --vcf [in.vcf|in.bcf|in.vcf.gz|in.bed.gz] — Your genotypes in VCF/BCF/BED format 🧬 This one is REQUIRED unless you're using --bed.
• --bed quantifications.bed.gz — Your quantifications in BED format 📊 REQUIRED unless you're using --vcf.
• --out output_file — The name of the output file 💾 REQUIRED, no skipping this one bestie 🙈
• --cov covariates.txt — The covariates you want to correct the data with ✨ REQUIRED unless you're using --normal.
• --qtl qtl_file [in.vcf|in.vcf.gz|in.bcf] — This one corrects your given phenotypes with your given genotypes 🦋 It takes two arguments:
  • The first is a text file listing genotype-phenotype pairs, separated by a space (e.g. snp1 gene1), with one pair per line 🍓 Each phenotype gets corrected for all the genotypes provided for that phenotype.
  • The second is a VCF file with the genotypes 🫶 The variant IDs in the qtl_file have to match the variant IDs in the VCF file, and the phenotype IDs have to match the --bed file.
  • Requires --bed.
• --normal — Rank normal transform the data 🌸 REQUIRED unless you're using --cov.

✨ EXAMPLES ✨

• Correct gene quantifications with technical covariates, rank normal transform the quantifications, and create a new bed file 💅

QTLtools correct --bed quantifications.bed.gz --out quantifications_corrected.bed --cov technical_covars.txt --normal

• Correct the gene quantifications for eQTLs 🧚

QTLtools correct --bed quantifications.bed.gz --out quantifications_corrected.bed --qtl eQTL_variant_gene_pairs.txt

✨ SEE ALSO ✨

Check out QTLtools(1) 📖

The QTLtools website is <https://qtltools.github.io/qtltools> 🌐

✨ BUGS ✨

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

Watch out for this on older versions, because your variant can quietly vanish from the analysis.

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

✨ CITATION ✨

Delaneau, O., Ongen, H., Brown, 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) and Halit Ongen (halitongen@gmail.com) 👑🌈

That's the whole page, bestie 🦋 Pulled from QTLtools version 1.3, dated 06 May 2020 💜