QTLtools-correct1

Usage

Overview

This mode corrects genotypes or phenotypes in VCF, BCF, or BED files with covariates provided and/or rank normal transforms the data and writes out the new corrected values to a file. This mode regresses out the covariates from the data, and writes the residuals to a file.

Options

--vcf [in.vcf|in.bcf|in.vcf.gz|in.bed.gz]

Genotypes in VCF/BCF/BED format. REQUIRED unless --bed.

--bed quantifications.bed.gz

Quantifications in BED format. REQUIRED unless --vcf.

--out output_file

Output file name. REQUIRED.

--cov covariates.txt

Covariates to correct the data with. REQUIRED unless --normal.

--qtl qtl_file [in.vcf|in.vcf.gz|in.bcf]

Corrects given phenotypes with the given genotypes. Takes two arguments. The first one is a text file listing genotype-phenotype pairs (separated by a space e.g. snp1 gene1), one pair per line. A phenotype will be corrected for all the genotypes provided for that phenotype. The second argument is a VCF file containing the genotypes. The variant IDs in the qtl_file must match the variant IDs in the VCF file, and the phenotype IDs must match with the --bed file. Requires --bed.

--normal

Rank normal transform the data. REQUIRED unless --cov.

Examples

o

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

o

Correct the gene quantifications for eQTLs

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

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>