When you sequenced a gene and you found a variant what should you do to know if this variant is known? In this I would first only like to focus on search through SNP databases. In this regard should you perform a search in each databases such as dbSNP, HGMD, 1000 genomes, ESP, and EXac to find if its known or are there better/easier ways to do this without any commercially software tool?
Dear Davide,
Thanks for your suggestion. I know of it, but I am still a little confused to whether such an overview will provide me with all known SNPs. More specifically, when I select my transcript of interest and click on the variation table and select all, I will get a lot of SNPs from various sources (dbSNP, HGMD, 1K etc). However, I still think I should use these sources seperately just to be sure nothing is missed. But, this is just a gute feeling. If you say Ensembl is continously updated by these sources, I could make use of Ensembl as a representative of these sources. A final question, am I correct if I say that ESP6500 and Exac are not yet integrated in Ensembl variation list?
Cheers,
R
Okay, so to be short, it incorporates the most important mutation databases.
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