.\"
.TH QTLtools "1" "November 2016" "1.0"
.SH NAME
QTLtools \- Tool set for molecular QTL discovery and analysis
.SH SYNOPSIS
.B QTLtools [\fImode\fR] [\fIoptions\fR]
.SH 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.
.SH MODE
.TP
\fBbamstat\fR
Calculate basic QC metrics for BAM/SAM.
.br
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.
.TP
\fBmatch\fR
Match VCF genotypes to BAM/SAM file.
.br
To ensure good match between the sequence and genotype data.
This is useful to detect sample mislabeling, contamination or PCR amplification biases.
.TP
\fBquan\fR
Quantification mode.
.br
To quantify exon and gene expression levels given a reference annotation such as GENCODE.
.TP
\fBpca\fR
Calculate principal components for a BED/VCF/BCF file.
.br
To perform Principal Component Analysis (PCA) on genotype or molecular phenotype data.
.TP
\fBcis\fR
cis QTL analysis.
.br
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.
.TP
\fBtrans\fR
trans QTL analysis.
.br
To map QTLs in trans.
This can be done either using a full permutation scheme or with a much quicker approximation.
.TP
\fBfdensity\fR
Functional density around QTLs.
.br
To measure the density of functional annotations around the QTL locations.
Useful to look at the degree of overlap between QTLs and functional annotations.
.TP
\fBfenrich\fR
Functional enrichment for QTLs.
.br
To measure how QTLs are enriched in any given functional annotations.
.TP
\fBrtc\fR
Regulatory Trait Concordance analysis.
.br
To co-localize collections of QTLs with collection of GWAS hits.

.SH OPTIONS
.TP
\fB\-\-help\fR
.br
Print help about options for the selected mode.

.SH EXAMPLE

\fBQTLtools\fR \fBbamstat\fR --help

\fBQTLtools\fR \fBbamstat\fR --bam HG00381.chr22.bam --bed gencode.v19.exon.chr22.bed.gz --filter-mapping-quality 150 --out HG00381.chr22.bamstat.txt
.br
\fBQTLtools\fR \fBmatch\fR --bam HG00381.chr22.bam --vcf genotypes.chr22.vcf.gz --filter-mapping-quality 150 --out HG00381.chr22.bamstat.txt
.br
\fBQTLtools\fR \fBquan\fR --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
.br
\fBQTLtools\fR \fBpca\fR --bed genes.50percent.chr22.bed.gz --scale --center --out genes.50percent.chr22
.br
\fBQTLtools\fR \fBcis\fR --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
.br
\fBQTLtools\fR \fBcis\fR --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
.br
\fBQTLtools\fR \fBcis\fR --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
.br
\fBQTLtools\fR \fBtrans\fR --vcf genotypes.chr22.vcf.gz --bed genes.simulated.chr22.bed.gz --nominal --threshold 1e-5 --out trans.nominal 
.br
\fBQTLtools\fR \fBtrans\fR --vcf genotypes.chr22.vcf.gz --bed genes.simulated.chr22.bed.gz --sample 1000 --normal --out trans.sample 
.br
\fBQTLtools\fR \fBfdensity\fR --qtl results.genes.significant.bed --bed TFs.encode.bed.gz --out density.TF.around.QTL.txt 
.br
\fBQTLtools\fR \fBfenrich\fR --qtl results.genes.significant.bed --tss results.genes.quantified.bed --bed TFs.encode.bed.gz --out enrichement.QTL.in.TF.txt 
.br
\fBQTLtools\fR \fBrtc\fR --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 
.br

.SH SEE ALSO
.BR https://qtltools.github.io/qtltools/
.SH AUTHOR
QTLtools was written by Olivier Delaneau, Halit Ongen and Manolis Dermitzakis.