Question: Difference between the two models in manta
1
gravatar for Jackie
2.3 years ago by
Jackie70
United States
Jackie70 wrote:

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

rna-seq manta • 714 views
ADD COMMENTlink modified 2.1 years ago by Chris Saunders170 • written 2.3 years ago by Jackie70
1

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.

ADD REPLYlink written 2.2 years ago by Mitch Bekritsky1.1k
1
gravatar for Chris Saunders
2.1 years ago by
Illumina
Chris Saunders170 wrote:

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.

ADD COMMENTlink written 2.1 years ago by Chris Saunders170
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1525 users visited in the last hour