Good Afternoon Ted: The command line arguments, and their discussion, are displayed by running the command with no arguments.
The liftOver operation is based on the map.chain file used with the command. To verify what results you might be able to find from the chain file, view that particular chain/net track in the genome browser. The chain file itself may not have multiple mappings for the location in question. A particular blat of a small sequence may indicate multiple mappings for that sequence, but the chain file mappings are constructed from a different alignment program, lastz: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.01.50.html with various filtering parameters to eliminate an over abundance of chain results. On the other hand, SNP mappings are performed with blat and multiple locations may result for SNP mappings. liftOver results may not produce the same multiple mapping result. When in doubt, you can re-map your SNP flanking sequences with blat to find the multiple mappings. --Hiram Ted Kalbfleisch wrote: > Hello, > > Is there any documentation that you can point me to that will fully > describe the command line options for liftover? I am working to map SNPs > between assemblies, and would like to be able to parameterize the command > line version to display multiple mappings, i.e. a single location in one > genome that maps to multiple locations in the second genome. I¹ve tried > using the multiple option, but liftover won¹t produce multiple mappings > that I know to exist from earlier BLAT analyses of a number of SNPs. Please > advise. > > Thanks and best regards, > > Ted > > Ted Kalbfleisch Ph.D. > Director of Bioinformatics Operations > Center for Genetics and Molecular Medicine > University of Louisville > 221 Baxter II > 580 South Preston Street > Louisville, KY 40202 > > 502-852-7495 > [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
