QTLtools-gwas1
Genome-wide association tests
Usage
QTLtools gwas
--vcf
[{in.vcf | in.vcf.gz | in.bcf | in.bed.gz}]
--bed
quantifications.bed.gz
--out
output.txt
[OPTIONS]
Overview
This mode runs a linear regression with every genotype vs. every phenotype.
Options
- --vcf [in.vcf|in.bcf|in.vcf.gz|in.bed.gz] ...
-
Genotypes in VCF/BCF/BED format. The DS field in the genotype FORMAT of a variant (dosage of the genotype 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 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 variant's chromosome 3 The variants'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
Examples
- o
-
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
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>
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).