QTLtools-rep1

Usage

Overview

This mode reads phenotype-genotype pairs that were identified in another dataset and checks association between the same genotype and phenotype in this dataset.

Options

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

Genotypes in VCF/BCF format, or another molecular phenotype in BED format. If there is a DS field in the genotype FORMAT of a variant (dosage of the genotype calculated from genotype probabilities, e.g. after imputation), then this is used as the genotype. If there is only the GT field in the genotype FORMAT then this is used and it is converted to a dosage. REQUIRED.

--bed quantifications.bed.gz ...

Molecular phenotype quantifications in BED format. REQUIRED.

--qtl external_qtls.txt ...

The file listing the QTLs identified in the external dataset. One phenotype genotype pair (separated by space, phenotype first) per line. REQUIRED.

--out filename.txt

The output file name. REQUIRED.

--cov covariates.txt

Covariates to correct the phenotype data with.

--normal

Rank normal transform the phenotype data so that each phenotype is normally distributed. RECOMMENDED.

Output file

output file

Space separated output file with the following columns.

1	The phenotype ID
2	The phenotype's chromosome
3	The phenotype's start position
4	The phenotype's end position
5	The phenotype's strand
6	The genotype ID
7	The genotype's chromosome
8	The genotype's start position
9	The genotype's end position
10	The p-value of the association
11	The slope of the association

Examples

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Replicate the results of dataset1 in dataset2, correcting dataset2 phenotype's with technical covariates and normal transforming them:

QTLtools rep --bed dataset2.bed.gz --vcf dataset2.bcf --cov dataset2.covariates.txt --qtl significant_qtls_dataset1.txt --normal --out rep_results.txt

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>