Fast and efficient QTL mapper for thousands of molecular phenotypes

Halit Ongen, Alfonso Buil, Andrew Anand Brown, Emmanouil T. Dermitzakis, Olivier Delaneau
<span title="2015-12-26">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: In order to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing. Results: We have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user-and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control
more &raquo; ... or multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted P-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot datasets can be now easily analyzed an order of magnitude faster than previous approaches. Availability and implementation: Source code, binaries and comprehensive documentation of FastQTL are freely available to download at http://fastqtl.sourceforge.net/
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btv722">doi:10.1093/bioinformatics/btv722</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26708335">pmid:26708335</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4866519/">pmcid:PMC4866519</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ygamesxp7vajhcsoal4ey35aze">fatcat:ygamesxp7vajhcsoal4ey35aze</a> </span>
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