Remapping SNPs to new genome build (bovine/porcine)

Question

[Barry Simpson]

Apologies if I sound lost here.

I am trying to update known SNPs from one genome build to another. A new porcine build has been out since February of this year and a new bovine build is in the process of being approved/curated at NCBI. Since the porcine genome data is out there, I will use that as my example, but as soon as the bovine comes out, I will have to repeat the process.

For porcine, I would like to take SNPs that are mapped to susScrofa10.2 and BLAST/BLAT/?? to positions on susScrofa11.1. I tried the NCBI remap tool and a few SNP positions as a test case, but the new positions indicated by the remap tool did not match up at all to when I actually BLASTed the markers in question. Ultimately, I need to perform this task on >1.5 million SNP markers, so any automation possible will be a necessity.

What tools can I use for this process? Is there already a tool out there that can do it? Keep in mind that neither of these has made it to UCSC yet, so methods that rely on files from there will not work. Also keep in mind that dbSNP is moving in September, making tools that rely on dbSNP a less desirable option. My searches thus far have not helped much, but maybe I am not approaching this from the correct angle.

I know this type of thing goes on every time a new genome build is announced, I just don't know where to start.

Thanks,

Barry

[ATpoint]

susScrofa10 is included in UCSCs liftOver tool. I would try to contact them and see if a chain file for 11.1 is available or in preparation.

Answer 1

[Emily]

We'll have version 11 of pig in Ensembl in the next release, coming out this week (fingers crossed!). You should be able to use the Assembly converter to convert the coordinates. Or, if they're known SNPs, we'll have remapped them so you can just use BioMart or the VCFs to pull them out.