Hi,

as the main developer and maintainer of shorah I'm really sorry that I didn't see this question before. Most questions and answers take place on GitHub and I'm also usually fast in responding to shorah related emails.

Freq: frequency

Pst:  posterior probability

Fvar: number of forward reads harbouring the variant

Rvar: number of reverse reads harbouring the variant

Ftot: total number of forward reads

Rtot: total number of reverse reads

PVAL: p-value

Qval: Benjamini-Hochberg corrected p-value 

I saw your publication on subpopulations in aMPV vaccines where you used both shorah and another tool. I was curious to hear your opinion on the software, also in comparison. For example ease of use, reliability, speed and whatever comes to your mind.

Best.

    Osvaldo

Thanks a lot!!

I had a very good experience with your software, just some troubles in installing it (during the installation some file were "missing" or apparently in the wrong folder but it wasn't a big problem) and then it was quaite easy to use it and the performances seemed really good. also the results were meaningful from both a biological point of view and comparing the with other software results.

Just to mention I've tried to redo a similar analysis on a database characteriazed by a huge difference (more than 3 log) in terms of coverage between the different region of the genome and the software reported a lot (something like 50% of the nucleotides) of SNV in the region with the high coverage. but I suppose that it is due to this bias in the coverage...when I tried to do the analysis using QuRE it simply consider only the first part of the genome stopping in the region with this "anomalous" coverage.

So I'm pretty sure that it is not a problem with your software!

Best