In the last weeks some people contacted us because they wanted to upload their exome-data to openSNP. While we started out with a focus on SNP-data (mainly because it’s much more abundant) providing support for exome-data has been on our ToDo-list for a couple of month now, so we did some work on it. Today we start with support for the data which is generated by 23andMe through their Exome-service.
So if you’ve got your exome sequenced through 23andMe you can now upload it to openSNP as well. Unfortunately there are some drawbacks right now:
- We only support upload for the VCF (Variant Call Format) and not for the BAM-file which contains the raw reads as well.
- We won’t parse all of your data. We will scan your exome for those SNPs which are already in the openSNP-dataset, but we won’t add any new ones to the web interface and won’t make other variants available for browsing on openSNP in the near future.
There are two main reasons for this limited feature-set:
- openSNP is our hobby project and we run with limited financial and computational resources. Basically right now we don’t have the computational power and storage to store and parse complete exome-BAM-files to deliver any benefit.
- Mining literature for known SNPs is easy, because a unique identifier exists for each SNP. This identifier is used in most publications and is seldom used for other purposes than referencing the SNPs. For Copy Number Variations etc. this isn’t that easy and we still haven’t had a good idea to get around this.
Nevertheless: If you’ve got your exome sequenced through 23andMe you can now upload your VCF-file. We will search for all known SNPs and make your genotypes available on the web-frontend of openSNP. And of course the complete VCF-file will be downloadable for anyone who is interested in it. Have fun uploading your data. And as always: Let us know if something doesn’t work as expected or if you have any further ideas for us.