Trying to resurrect this project and put it back on the web - missing some .json files

[matthiasschabel]

Wondering if anyone knows if there is a more complete repo with following files: data/Genotype.json, data/Rsnum.json, data/Medicine.json, data/Genoset.json? Or has successfully gotten this project running?

[exander77]

Hello, I don't run the project currently. What do you want to do with it?

[matthiasschabel]

I used it to analyze VCF files for some family members but it appears to no longer be online. I was hoping to use it to do the same for some friends who have WGS data.

[cariaso]

@matthiasschabel you may be interested in https://patientuser.com/

[matthiasschabel]

That web site doesn't appear to be functional? In any case, I am a bit lukewarm on handing out WGS data to random web servers...

[cariaso]

That web site doesn't appear to be functional? In any case, I am a bit lukewarm on handing out WGS data to random web servers...

we're pretty small, and I'm currently doing a rebuild. should be back up shortly.

but perhaps we're less random than you imagine. I'm the guy who wrote promethease
https://snpedia.com/index.php/User:Cariaso
and this is my attempt to reimagine how to engineer for WGS.

[matthiasschabel]

Cool - sorry I wasn't more thorough in looking through the project! I'll give it a closer look when it's back up.

[exander77]

@cariaso @matthiasschabel I liked my idea of in browser vcf analysis, it would be great to work with somebody who really understand the vcf and snp to improve this. It basically downloads databases for SNP and criteria and then stream process gzipped vcf file.

I originally backed up SNPedia when it was looking bad with it and wrote this tool. It requires data to process. If @cariaso project maintains good data for analysis We could resurrect it. And I would really like somebody with the deeper knowledge to look into how I process it. Would you be willing to back it with data and maybe integrate it your project as "no data leaves your computer" for vcf analysis?

[exander77]

I pushed all data and all sources I had, but it was just hobby project I did back in 2021. So work in progress.

[exander77]

I will resurrect the website tomorrow.

[cariaso]

If @cariaso project maintains ...

My effort focuses on non-VCF input files which are 100GB+, and in other ways probably not as well aligned with what you may have in mind.

[exander77]

If @cariaso project maintains ...

My effort focuses on non-VCF input files which are 100GB+, and in other ways probably not as well aligned with what you may have in mind.

Yes, I wouldn't dream doing alignment to VCF in browser currently. Not that it is entirely out of the question in the future. Last time I did it it was back in 2021 and I had 64 threads running it 2 days.

I would really like good database I can match VCF against.

Btw, I renewed the project functionality: https://geno.openmethease.com/

[matthiasschabel]

In terms of data, are you talking about genomes? I have personal WGS data for a bunch of family members, have been playing with GATK and some other bioinformatics tools, looking at haplotyping to pull out de novo mutation lists, etc... I am not much of a JavaScript programmer, but am pretty good with Python (and C++, MATLAB) so could probably contribute to backend work.