HaploQA is a software platform that provides interpretation of genotype calls from the Mouse Universal Genotyping array platforms (Mega-/Giga- MUGA) that are available from Neogen Genomics (Morgan et al., 2015). The software allows for direct upload of sample and genotype data, sample annotation, and organization by users. The software interprets genotype calls and uses established Hidden Markov Models that were generated by Dr. Gary Churchill’s laboratory to generate haplotypes with negative log likelihood scoring. There are additional options for interfacing with the data through a web-based graphics, links out to widely used genome browsers, data/image/report downloads, and options for making the data public. If you want to read more about MUGA platforms the following is a great resource:
To get started with HaploQA, you may browse the public data listed below. However, if you wish to upload your own data, you'll need to have an account. You can login in the upper right corner if you already have one; otherwise, please send an email to firstname.lastname@example.org to have one set up for you.