Difference between the two models in manta

Question

[Jackie]

What is the difference between the manta disease model (--tumorBam) and germline model (--bam)? i.e, different calling algorithms, different filtering criteria? Is there some detailed documentation on that?

Thanks

[Mitch Bekritsky]

Have you checked the method overview or the methods PDF in the repo? Manta can run on germline only, tumor only, and paired tumor/normal subtractions. I believe it's methods PDF explains most of the details.

There's also the preprint on the biorXiv, which has a pretty extensive supplement.

Answer 1

[Chris Saunders]

The short answer is that the germline model assumes a diploid sample with corresponding allele frequencies. The tumor-only model assumes the variant could occur at any allele frequency. The best starting point for a high-level overview is the user guide:

https://github.com/Illumina/manta/tree/master/docs/userGuide

And the methods writeup for more details:

https://github.com/Illumina/manta/tree/master/docs/methods/primary

This is a latex doc you'll need to clone and render for the latest version. As described above, the supplement provided with the pre-print or final publication are both very good starting points.