QTLtools rep - Replicate QTL associations in an independent dataset
QTLtools rep --bed quantifications.bed.gz --vcf
[in.vcf|
in.vcf.gz|
in.bcf] --qtl
qtls_external.txt --out output.txt [OPTIONS]
This mode reads phenotype-genotype pairs that were identified in another dataset
and checks association between the same genotype and phenotype in this
dataset.
- --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
- 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 |
- o
- 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
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])