Convert Soft Liftover Usage

Question

[Liyf]

I have a problem with liftOver. I have 300,000 snps to convert from hg18 to hg19,so I use liftOver. I download it in my own computer and run it.I also download the chain which is hg18 to hg19. I found that it can handle most of snps, but will fail about 10,000 snps. I search the failed snps in NCBI, and found they are actually in NCBI, and have position of hg18 and hg19. How can I do do convert the remainder snps? I want to handle them in batches.

Answer 1

[Bert Overduin]

If the failed SNPs all have rs IDS, you should be able to retrieve their current position from Ensembl using either BioMart or the Perl API, provided Ensembl has been able to map them to GRCh37 (a.k.a. hg19).

[Liyf]

Thanks. I am new, so I have not used BioMart and Perl API yet. I will try. Any advise? I have no one to teach me around, so I have to learn them all by myself.

[Bert Overduin]

In that case, I would start with BioMart. Please have a look at the BioMart videos on YouTube to get an idea how to work with it: http://www.youtube.com/user/EnsemblHelpdesk#p/u/4/DXPaBdPM2vs and http://www.youtube.com/user/EnsemblHelpdesk#p/u/6/paC3sOANSJA. I hope this helps. Questions regarding Ensembl BioMart can be directed to the Ensembl Helpdesk ([e-mail]).