rare-disease-wf VS hlatyping

Feel free to reach out, username at berkeley edu.

In open source bioinformatics we strive for reproducible science, which can be difficult in a field with tons of different methods and tools. One approach is to use a workflow language such as Nextflow [0] and Docker/Singularity such that the entire analysis is reproducible, see e.g. [1].

There is a vibrant community around Nextflow workflows called nf-core [2] which has a rare disease workflow in development [3], come join our slack!

[0] - https://nextflow.io

[1] - https://github.com/brentp/rare-disease-wf

[2] - https://nf-co.re

[3] - https://nf-co.re/raredisease

Here's a post I made on reddit about how to do exactly this:

https://www.reddit.com/r/Nebulagenomics/comments/nhjfpa/how_...

You use the VCF and a java project called the Exomiser, and it will give you output files with all the pathogenic variants marked

In my case and is the case with a lot of rare diseases you could have unique pathology and mutations in a certain gene but that don't show up as pathogenic in clin var. For example my family has a lot of autoimmune diseases and as expected my HLA genes are totally trashed. However none of these mutations have ever been seen and flagged before especially was WGS is so new.

If you only have a list of genes and the genomizer will give you a list of the genes that are the most heaviy affected, you can put them into this app to get some further data and idea about what kind of tissue expression or rare disease spectrums you may be dealing with: https://maayanlab.cloud/Enrichr/

sadly the reality is though you can have all that and it almost puts you at a disadvatnage with doctors because you look crazy and sus claiming you have some HLA mutation or whatever. Who told you that? Oh well I data mined it...uh huh sure....honestly to get it back into the medical system and to be taken seriously you'd probably have to get a doctor to retest it, for example I can can spin this up to get my HLA alleles from my fastq https://github.com/nf-core/hlatyping

But no doctor is going to put that in my medical record until I convince them to run a blood test for the same damn thing.

if anyone wants to help me with my own genetic search woes and help me out or know solutions please let me know. if you want to help me publish or add to that guide somewhere let me know - i asked nebula if they wanted to print it on the blog and they said the'd be interested but I just never cleaned it up