QTLtools correct - Corrects genotypes or phenotypes with the
provided covariates
QTLtools correct --vcf
[in.vcf|in.vcf.gz|in.bcf] | --bed
in.bed.gz --cov covariates.txt | --normal --out
output.txt [OPTIONS]
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.
- --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.
- 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
QTLtools(1)
QTLtools website: <https://qtltools.github.io/qtltools>
- o
- 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. 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 (olivier.delaneau@gmail.com), Halit Ongen
(halitongen@gmail.com)