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Big Data App to Explore Genomes for Clinical Relevance, Rare Variants, Drug Response, etc (Free)

nandixon

Senior Member
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@Brandit, I'm guessing that's a miscall by 23andMe. dbSNP gives the frequency for the variant (A --> G) at only 1 in 77,108 alleles, and also gives a study showing it to be pathogenic for Charcot-Marie-Tooth disease, albeit with a mild course. OpenSNP (with data mostly from 23andMe users) on the other hand gives a frequency of 20%, so that seems off.
 
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This particular one caught my eye because it is mitochondrial in nature. I think my paternal grandmother had Charcot so it may be possible. I suppose that's a dead end if one database says extremely rare and one say 1 in 5
 

kday

Senior Member
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Fixed a lot of bugs and made some important fixes so 23andMe and Ancestry data a lot more accurate the past week or so. I haven't fixed some of the bugs mentioned above or lower priority bugs yet. But those are next!

I also noticed some people have Genos data, and realized my app was not compatible because Genos data is not gzip compressed.

Genos .vcf files are compatible now, and it really surprised me how fast these exome files process. Literally within some seconds! Much faster than 23andMe/Ancestry data.
 
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While I'd like to think I'm solving the "how do you make tools accessible to everyone" dilemma, it's harder to solve how do you make it easy to understand for those that are less technically minded or have limited knowledge about genomics.
I think it's amazing that you built this tool. The fact that you're sharing it openly says a lot about you :)
Designing interfaces that make it simpler for people to understand - that's an art form.
Would you be open to someone else helping you to do that?
I don't think it's necessary for you to have all the skills needed to make this work. Collaborate if you can, it's great to collaborate.
 
Genos .vcf files are compatible now, and it really surprised me how fast these exome files process. Literally within some seconds! Much faster than 23andMe/Ancestry data.
I've uploaded my genos file unzipped on my computer to .vcf file. The upload seems to work ok, however it runs a couple seconds, creates the screen, but all options have the following message " No variants were found in the section. Consider this a good thing! "

Is there something else I should do? My 23 and Me file processed ok a few weeks ago.
Thanks,
Pat
 

kday

Senior Member
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I've uploaded my genos file unzipped on my computer to .vcf file. The upload seems to work ok, however it runs a couple seconds, creates the screen, but all options have the following message " No variants were found in the section. Consider this a good thing! "

Is there something else I should do? My 23 and Me file processed ok a few weeks ago.
Thanks,
Pat
Strange. If you PM me I can take a look at this and fix the issue if you are ok with sharing your data. It should work with Genos files though. How long ago were you sequenced?
 
Strange. If you PM me I can take a look at this and fix the issue if you are ok with sharing your data. It should work with Genos files though. How long ago were you sequenced?
My apologies for the delay, stumbling back from a crash... The Genos download file is named kit#_annotated.vcf.zip

Other formats that can be downloaded are PROMETHEASE, BAM/FASTQ. Sequenced in November 2017.
 

Moof

Senior Member
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Could you please share how you solved this? Thanks!
There was nothing very technical about it – I just duplicated the file and then deleted the additional '.vcf' extension on the copy! I wasn't really expecting it to work, to be honest, but it did. The Mac will probably ask if you really want to change the extension, at which point you just click Yes.

This is how they now look in the file list, with the one ending '.gz' being the edited version that I uploaded.


Screenshot 2019-10-24 at 19.28.44.png

Edited to add: If your Mac doesn't show file extensions, go to Finder Preferences and click the Advanced tab. Check the Show all File Extensions box.
 
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@Moof Thanks! That’s what I did too. Managed to upload the file in the app, but there was no results, except for one variant...🤔

Edit: It’s working now—got the full report!👍
Edit 2: The problem was that I uploaded the indel file and not the snp...😬
 
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