torus is a free software package that implements a computational procedure for discovering molecular QTLs incorporating genomic annotations.

The following C/C++ libraries are required for compiling the source code

• GNU GSL library
• Zlib library
• Boost C++ library

• -d data_file: the data_file should be compressed in gzip format and contain summary statistics from single SNP association analysis. Currently, two formats are supported: 1) gzipped MatrixEQTL output single SNP association result;

2. pre-computed Bayes factors based on single SNP association tests. If 2) is used, it is important to specific --load_bf in the command line.

• -smap snp_map: gzipped SNP position files
• -gmap gene_map: gzipped Gene position (transcription start site) file With both files specified, torus will control for SNP distance to transcript start site (TSS)

• -est: output the estimates of enrichment parameters and their confidence intervals
• -qtl: perform Bayesian FDR control, and output the result
• -dump_prior: compute SNP-level priors using the estimated enrichment estimates for each locus

We provide two real data tutorials to illustrate the usage of torus for QTL discovery. They eQTL data from the GEUVADIS project and the GTEx liver tissue. The tutorials can be found in the [examples] (https://github.com/xqwen/torus/tree/master/examples/) directory.

• Wen, X. Effective QTL Discovery Incorporating Genomic Annotations. bioRxiv doi:10.1101/032003.