NAME¶
QTLtools - Tool set for molecular QTL discovery and analysis
SYNOPSIS¶
QTLtools [mode] [options]
DESCRIPTION¶
QTLtools is a tool set for molecular QTL discovery and analysis. It allows user
to go from the raw sequence data to collection of molecular Quantitative Trait
Loci (QTLs) in few easy-to-perform steps.
MODE¶
- bamstat
- Calculate basic QC metrics for BAM/SAM.
To check the quality of some sequence data by counting the number of reads
mapped to the reference genome and falling within a reference
annotation.
- match
- Match VCF genotypes to BAM/SAM file.
To ensure good match between the sequence and genotype data. This is useful
to detect sample mislabeling, contamination or PCR amplification
biases.
- quan
- Quantification mode.
To quantify exon and gene expression levels given a reference annotation
such as GENCODE.
- pca
- Calculate principal components for a BED/VCF/BCF file.
To perform Principal Component Analysis (PCA) on genotype or molecular
phenotype data.
- cis
- cis QTL analysis.
To map molecular Quantitative Trait Loci (mQTLs) in cis (i.e. proximal to
the phenotype). This mode extends FastQTL by including two additional
options: (i) to study groups of phenotypes such as genes containing
multiple exons or (ii) to perform conditional analysis in order to
discover multiple mQTLs per phenotype.
- trans
- trans QTL analysis.
To map QTLs in trans. This can be done either using a full permutation
scheme or with a much quicker approximation.
- fdensity
- Functional density around QTLs.
To measure the density of functional annotations around the QTL locations.
Useful to look at the degree of overlap between QTLs and functional
annotations.
- fenrich
- Functional enrichment for QTLs.
To measure how QTLs are enriched in any given functional annotations.
- rtc
- Regulatory Trait Concordance analysis.
To co-localize collections of QTLs with collection of GWAS hits.
OPTIONS¶
- --help
-
Print help about options for the selected mode.
EXAMPLE¶
QTLtools bamstat --help
QTLtools bamstat --bam HG00381.chr22.bam --bed
gencode.v19.exon.chr22.bed.gz --filter-mapping-quality 150 --out
HG00381.chr22.bamstat.txt
QTLtools match --bam HG00381.chr22.bam --vcf
genotypes.chr22.vcf.gz --filter-mapping-quality 150 --out
HG00381.chr22.bamstat.txt
QTLtools quan --bam HG00381.chr22.bam --gtf
gencode.v19.annotation.chr22.gtf.gz --samples HG00381 --out-prefix HG00381
--filter-mapping-quality 150 --filter-mismatch 5 --filter-mismatch-total 5
--rpkm --no-merge
QTLtools pca --bed genes.50percent.chr22.bed.gz --scale --center
--out genes.50percent.chr22
QTLtools cis --vcf genotypes.chr22.vcf.gz --bed
genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --nominal
0.01 --region chr22:17000000-18000000 --out nominals.txt
QTLtools cis --vcf genotypes.chr22.vcf.gz --bed
genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --permute
1000 --region chr22:17000000-18000000 --out permutations.txt
QTLtools cis --vcf genotypes.chr22.vcf.gz --bed
genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --mapping
permutations_all.thresholds.txt --chunk 12 16 --out conditional_12_16.txt
QTLtools trans --vcf genotypes.chr22.vcf.gz --bed
genes.simulated.chr22.bed.gz --nominal --threshold 1e-5 --out trans.nominal
QTLtools trans --vcf genotypes.chr22.vcf.gz --bed
genes.simulated.chr22.bed.gz --sample 1000 --normal --out trans.sample
QTLtools fdensity --qtl results.genes.significant.bed --bed
TFs.encode.bed.gz --out density.TF.around.QTL.txt
QTLtools fenrich --qtl results.genes.significant.bed --tss
results.genes.quantified.bed --bed TFs.encode.bed.gz --out
enrichement.QTL.in.TF.txt
QTLtools rtc --vcf genotypes.chr22.vcf.gz --bed
genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --hotspot
hotspots_b37_hg19.bed --gwas-cis GWAS.b37.txt
permutations_all.significant.txt --normal --out rtc_results.txt
AUTHOR¶
QTLtools was written by Olivier Delaneau, Halit Ongen and Manolis Dermitzakis.