We are evaluating the liftOver tool for converting SNPs, that our researchers have found, from hg18 to hg19 (IOW, not ones that are in dbSNPs). As a test I ran the hg18 dbSNPs 130 through liftOver, then compared the results to the hg19 dbSNPs 130.
My results: Starting: 18,833,531 Converted by liftOver: 15,423,712 Match Official position: 11,788,968 Failed to map: 3,409,819 Mapped to "wrong" location: 3,634,744 1: Should my experiment have worked? "Should" the liftOver tool have gotten all the SNPs to their official hg19 locations? 2: I'm not really worried about the SNPs that failed to map, but have ~20% of the SNPs map to the wrong location is kind of concerning. What is your expected error rate? Thank you, Greg _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
