This online tool can be used to extract and plot the Orion scores of two sets of regions or two sets of variants. Input coordinates should be in BED format (0-based, inclusive start, exclusive end) and correspond to hg19. A higher Orion score corresponds to a higher degree of intolerance.
The full set of scores are available for download here.
For more information, read the manuscript.
To test for enrichment of case mutations in Orion regions, download the Orion regions bed file and the Orion scorespace file (the Orion scorespace file is a BED file denoting the coordinates across which the Orion scores are defined). Using bedtools subset your case and control variants only to those falling in the Orion scorespace, by intersecting your case and control BED files with the Orion scorespace file. This will result in a set of control variants falling in the Orion scorespace and a set of case variants falling within the Orion scorepsace.
Following this, tally the number of case variants falling within the Orion regions out of all the case variants in the scorespace and the number of control variants falling within the Orion regions out of all the control variants in the scorespace. With this in hand, you can calculate a Fisher's Exact Test P Value for enrichment of case mutations in the Orion regions.
Gussow AB, Copeland BR, Dhindsa RS, Wang Q, Petrovski S, Majoros WH, et al. (2017) Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics. PLoS ONE 12(8): e0181604. https://doi.org/10.1371/journal.pone.0181604
For bug reports, questions, or comments, please contact Ayal Gussow (firstname.lastname@example.org).