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
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written
by
Jackie
1 answer
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.
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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.