Basic information

• Homepage
• Download & Installation
• Compilation examples
• GitHub / QTLtools
• QTLtools figures

Analyses

• Preparing input files
• Overview of QTLtools
• [bamstat] QC the sequence data
• [mbv] Sequence to genotype matching
• [quan] Quantify gene expression
• [pca] Perform PCA on data
• [cis] Discover QTL in cis [nominal pass]
• [cis] Discover QTL in cis [permutation pass]
• [cis] Discover QTL in cis [conditional pass]
• [trans] Discover QTL in trans [full pass]
• [trans] Discover QTL in trans [approx. pass]
• [fdensity] Annotation density at QTLs
• [fenrich] Enrichment of QTLs in annotations
• [rtc] Overlap QTLs with GWAS hits

Man Pages

• Overview of QTLtools
• [bamstat] Calculate basic QC metrics for BAM/SAM
• [mbv] Sequence to genotype matching
• [pca] Perform PCA on data
• [correct] Covariate correction of BED or VCF file
• [cis] Discover QTL in cis
• [trans] Discover QTL in trans
• [fenrich] Enrichment of QTLs in annotations
• [fdensity] Annotation density at QTLs
• [rtc] Colocalization analysis of QTLs and GWAS hits
• [rtc-union] Find the union of QTLs
• [extract]Extract all data from the provided files
• [quan] Quantify gene and exon expression
• [ase] Measure allele specific expression
• [rep] Replicate QTLs in an independent dataset
• [gwas]Correlate all genotypes with all phenotypes

Credits

• Dr Olivier DELANEAU, UNIGE
• Dr Halit ONGEN, UNIGE
• Prof. Manolis DERMITZAKIS, UNIGE

References

• QTLtools: a complete tool set for molecular QTL discovery and analysis. Nat Commun 8, 15452 (2017).
• Estimating the causal tissues for complex traits and diseases. Nat Genet. 2017;49(12):1676-1683.
• MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets. Bioinformatics 33(12), 1895 2017.