Frequently_Asked_Questions

Frequently asked question by my fellow bioinformaticians on this pipeline

What is cold storage?

On most clusters, a difference is being made between repositories designed to IO-intensive computations (hot storage), and repositories designed to archive (cold storage). Locally, system administrators allow (or not) the users to compute on archive-designed repositories.

Yet, copying all your fastq files at once before starting to work is time consuming and requires two copies of all your fastq files at the beginning of your work. Let Snakemake handle both copy creation and removal. This will save you time!

I have seen a typo/coding error.

You should not. I am very happy to improve myself, this code, and to help you get more confidence in yourself. You have found a mistake? Open an issue. CHEERS and THANK YOU!

I want to change/add/replace anything in your code. Can I?

You can open an issue, or fork this git repository, and make your own path. You are likely to have very good reasons to do so. Who knows, maybe you'll make a pull request?

Frequently asked questions by my fellow biologists on this pipeline

Does this pipeline remove any variant?

With default parameters : No.

However, depending on the parameters set by the bioinformatician, you may have some filters applied. Ask your bioinformatician to be sure.

Did you checked that there is not lost variant?

Yes. This information is available in the MultiQC report: you can see the number of reads recieved by Snpeff (the original ones) and compare this number with the ones provided by SnpSift few steps further.

Why not Annovar?

Annovar provides its own annotations. SnpEff and SnpSift uses all annotations from official databases. This means these two will always be more up-to-date than Annovar. Thus, installation and use of Annovar is not possible without the consent of its developer : the code is not available for anyone by anyone. This means fewer people can submit corrections and improvements.

In addition, SnpEff and SnpSift are faster.

And finally, why not Jannovar? Why not VEP? Why not ... At the end, you have mostly the same information. SnpEff/SnpSift are, by design, the most simple and straightforward to use.