Many of the UCSC genome tools are available for download for use locally on your UNIX system. liftOver is an example of one such tool. To download, go to their apps download page, select your operating system, and then click on the liftOver link. Here are links for liftOver_linux.x86_64 and liftOver_linux.x86_64.v287. For some reason, I could only get the linux.x86_64.v287 version to work on my system. Once downloaded, make it executable.
The next step is to get the required chain files needed to convert from one genome build to another. All UCSC genome builds are listed here and you can select the desired "LiftOver files" link under the genome build that you want to convert from. This will take you to a downloads page with links to the chain files. Chain files are appropriately named so you know what builds you are converting to and from. For example, hg19ToHg18.over.chain.gz is the chain file needed to convert from hg19 to hg18. Once downloaded, unzip the file for use.
To run liftOver, the useage is:
liftOver oldFile map.chain newFile unMapped
oldFile is the file you want to convert from
map.chain is the chain file used to convert from one build to another
newFile is the converted file you want to create
unMapped is a file that contains all the unmapped positions
For more details on usage, just type liftOver in the command line.
Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.