STRchive disease loci regions file

[hdashnow]

Hi @Dhaksnamoorthy and @sowpati,

Thanks for creating this awesome method!

I'm working on creating a ATaRVa regions files for the STRchive.org rare disease loci. This will eventually be added as a resource on the website.

I would love some feedback!

Principles (after some discussion with @avvaruakshay):

• For loci with multiple pathogenic motifs there is a separate row for each motif with the same coordinates
• For compound/compled loci with non-pathogenic flanking motifs these are in a separate row with appropriate flanking coordinates
• I added an ID column. I know ATaRVa doesn't require one, but it's something you might consider including in the VCF output down the track

Here is a link to the code/files. Let me know what you think.
dashnowlab/STRchive#185

[sowpati]

Hi @hdashnow,

Thanks so much for the positive feedback, and for adding atarva BED files to STRchive. We'll also try testing this out on a few samples to see if the output is as expected.

Your suggestion about adding extra info is a good one. In the upcoming version, we will add an option to include all extra BED columns in the VCF output (using the name of the columns if header is provided).

Re: multiple motifs with the same coordinates - I feel having one entry should be enough (with any representative motif). ATaRVa should be able to report the correct motif composition, particularly when all the variations are of the same motif size.

Re: compound/flanking motifs - Even here, having one entry including the flanks might work but we'll have to test it out.

More importantly, I don't know what's the preferred approach by the end users. Your inputs on how atarva should handle/report such loci will be greatly appreciated.

[hdashnow]

Hi @sowpati,

Sorry for my slow response. I've been travelling and am just now getting back to this.
In the meantime, @avvaruakshay tested the flanking and multiple-motif points. He suggested I should include flanking motifs and agreed with you that reporting multiple motifs at the same coordinates is not necessary. I've made those changes and will make this available on STRchive soon.

I'll be sure to share more feedback as I work with the files more.

Warm regards,
Harriet

[hdashnow]

The Atarva catalog files are now available for all STRchive loci and will be updated automatically as new loci are added. You can find them here:
https://strchive.org/loci/#downloads

Let me know if you notice any issues with the format or coordinates.