Provided by: qtltools_1.1+dfsg-2build1_amd64 
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
SEE ALSO
https://qtltools.github.io/qtltools/
AUTHOR
QTLtools was written by Olivier Delaneau, Halit Ongen and Manolis Dermitzakis.