We’ve heard lots of requests from customers not only to provide them with powerful methods for detection variants across multiple experiments (or phenotypes, or organisms, or lines), but for unifying all of this data to find knowledge that spans these experiments.
Of course we have our variant calling workflow, just as we integrate with other variant calling workflows. All of these produce GenomeQuest-native browsable, mineable, and queryable databases. And because of the GQ Engine, we can easily combine sets of 10s or 100s or even 1,000s of these variant databases into a single queryable entity with “web-speed query performance.”
Nevertheless, while our customers get the benefit of the combined data, they often ask for more. So today I jumped in to the APIs of GenomeQuest and tried to address the simple problem of building a table of SNPs that span a series of experiments. Each SNP should have the specific allele called for each experiment in which it was found. A simple little table designed to be the input into any of a number of linkage disequalibrium mapping packages. I made a GQ Plug-in: 5 lines of code to make it accessible in the user interface, and another 100 lines of code (I’m wordy) on the back-end to build the table and present it. And so, the multi-experiment haplotype table is born. I might even convince the development team to include it in our next live push.
If you want to hear more or check out the code, drop me a line.
Richard J. Resnick
VP Software and Services
