QTLtools gwas - Genome-wide association tests
QTLtools gwas --vcf
[in.vcf|
in.vcf.gz|
in.bcf|
in.bed.gz] --bed
quantifications.bed.gz --out output.txt [OPTIONS]
This mode runs a linear regression with every genotype vs. every phenotype.
- --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
- 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 |
- 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
QTLtools(1)
QTLtools website: <
https://qtltools.github.io/qtltools>
Versions up to and including 1.2, suffer from a bug in reading missing genotypes
in VCF/BCF files. 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, in which case genotypes for all the samples are set to missing,
effectively removing this variant from the analyses.
Please submit bugs to <
https://github.com/qtltools/qtltools>
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>
Olivier Delaneau (
[email protected]), Halit Ongen
(
[email protected])