Hello, I am using the command line liftOver tool (for 64-bit linux) together with the chain file hg18ToHg19.over.chain to convert genome coordinates from hg18 to hg19. Command line tool fails to convert most of the single position coordinates, in other words coordinates with the same start and end positions cannot be converted.
Below is an example line from the input file: chr17 7520197 7520197 And the output in the unmapped file for these coordinates is: #Deleted in new chr17 7520197 7520197 However, when I use the web-based version (http://genome.ucsc.edu/cgi-bin/hgLiftOver), the same data is successfully converted from hg18 to hg19. Here is the input that works for the web-based version: chr17:7520197-7520197 And the conversion result is: chr17:7579472-7579472 Do you have an idea why the command line tools does not work for such coordinates. Are the default parameters of the web-based version different than the command-line version? Or, can it be a bug in the command line tool? Or, maybe I am missing some point. Thanks, Onur Sumer Computational Biology Center, Memorial Sloan Kettering Cancer Center _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
