I am trying to compare array snp calls to ngs snp calls, by using the position of the genotype. However the builds used differ, so I would like to make a liftover of the array data to meet the ngs data. USCS offers a liftover from e.g. build 18 to 19, however I havent been able to find a site where I can do a liftover from e.g. build 19.p1 to 19.p9. Is there someone out there that can help me ? Thanks.
You can ask the author of liftOver for help~maybe he can generate the input file (19.p1To19.p9.over.chain) required by LiftOver for you.
Although not what you asked for, but my solution would be (and have actually been) to either i) blast/blat the probe-seqs against the genome that you aligned you NGS data to or ii) realign the NGS data to a genome you can use liftOver on.
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