2.2 years ago by
FWIW I recently made a SNPlocs package for dbSNP Build 149 (the latest dbSNP build) but it's only available in BioC devel (i.e. BioC 3.5, requires R 3.4):
I actually highly recommend that you upgrade your installation to use BioC devel if you're planning to do any serious work with the SNPlocs package because these packages have been refactored to allow much faster data access.
There is currently no established schedule for updating these packages. These packages are big, making them is time-consuming, and they are not heavily used, so it's kind of hard to keep up with every dbSNP new build and it would also be hard to justify spending too much resources on doing that (we have to choose our priorities). However, if the community starts to express more interest in these packages, I will update them more often e.g. make a new one for every other dbSNP build.
You could follow the instructions in SNPlocs.Hsapiens.dbSNP***.GRCh38/inst/tools/README.TXT to make your own SNPlocs package. Some users have done it before e.g. https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP142.GRCh37. But as I said, this procedure can be tedious and time-consuming. Note that if you decide to do so, I would highly recommend that you follow the procedure described in the README.TXT file of the SNPlocs.Hsapiens.dbSNP149.GRCh38 package because the procedure has changed significantly in BioC 3.5. In particular it's faster now: it takes about 3h instead of 14h. The README.TXT file in SNPlocs.Hsapiens.dbSNP149.GRCh38 describes the most up-to-date version of this procedure. And yes, the resulting package should work for injection in a BSgenome object, and the SNPs should land at the correct positions.
modified 2.2 years ago
2.2 years ago by
Hervé Pagès ♦♦ 13k