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.

1.0                                               November 2016                                      QTLtools(1)