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.