Hi Natalie, To find chain files on the website, go to the homepage, and then hit the "downloads" link on the left-hand side of the page, then click "Human", scroll to "Mar. 2006 (hg18)" and click "LiftOver files". It should take you to this page, which contains all of the over.chain files from the hg18 (b36) assembly to other assemblies:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/ Your input files need to be in one of the formats listed in the usage statement for liftOver (just type "liftOver" with no arguments at the command line to see the usage statement). I'm not sure what .gen and plink files are; you will likely need to convert them to one of the accepted input formats, such as BED. Data format descriptions are here: http://genome.ucsc.edu/FAQ/FAQformat.html If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/03/11 04:36, Natalie Van Zuydam wrote: > Hi there, > > I'm looking to convert a hg18 (b36) set of SNP coordinates to a hg19 > (b37) set of chromosome positions. I cannot find the correct chain files > on the website. I've got my files in .gen and binary plink files, I'm > not sure which option to use for the linux liftOver tool? > > Many thanks, > Natalie > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
