HaploQA is a software platform that provides interpretation of genotype calls from the Mouse Universal Genotyping array platforms (including 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:

Morgan AP et al.
The Mouse Universal Genotyping Array: From Substrains to Subspecies.
G3 (Bethesda). 2015 Dec 18;6(2):263-79. doi: 10.1534/g3.115.022087.
PMID: 26684931; PMCID: PMC4751547


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 either login to your account if you already have one, or you can create a new account using the 'Sign Up' option in the top left. Please contact us at haploqa@jax.org if you have any questions.