dbsnp RSIDs on canFam6
Batra, Sajeev
Gerardo Perez
Hello, Sajeev.
Thank you for your interest in the UCSC Genome Browser and for your inquiry.
Unfortunately, there is no dbSNP track available for canFam6. As of September 1, 2017, NCBI phased out support for non-human organisms in dbSNP and dbVar and now supports only human variation data: https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/09/phasing-out-support-for-non-human-genome-organism-data-in-dbsnp-and-dbvar/
We do provide an EVA SNP Release 8 track for canFam3, which you can view here: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=canFam3&g=evaSnp8
It is not recommended to use LiftOver to convert SNPs between two assembly versions. Using LiftOver to convert a very small region, especially a single-base SNP, is not always a trivial task, as the alignment may not receive a high enough score to be considered a successful conversion. Instead, the recommended process to convert a SNP's coordinates between assemblies is to use a SNP track to search for each rsID on the target genome assembly. More information about SNP coordinate conversion is available in our FAQ: https://genome.ucsc.edu/FAQ/FAQreleases.html#snpConversion
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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