On Tue, May 31, 2011 at 4:11 PM, Brooke Rhead <[email protected]> wrote: > Hi Anoma, > > Run the liftOver command without arguments to see the usage statement. > The correct command line is: > > liftOver oldFile map.chain newFile unMapped > > (In addition to the newFile, you need to include a file for unmapped > regions.) Also, you will need to use the "-gff" option, since your > input file is in .gff format. So your command line should look like: > > liftOver -gff oldFile hg18ToHg19.over.chain newFile unMapped > > Note that the liftOver tool will not necessarily get you the same > mappings in hg19 that appear in the build 132 SNP tracks. > > I hope this is helpful. If you have further questions, please feel free > to contact us again at [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > On 05/30/11 09:22, Anoma Jaya wrote: >> Hi, >> >> I want to convert coordinates of SNPs filtered using hg18 to coordinates of >> hg19 with liftOver. I got input data files >> from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/ link. >> Can U please tell me what is the command line that I should give in the Linux >> terminal to execute the task? >> >> ( I gave >> $ liftOver oldFile hg18ToHg19.over.chain newFile >> >> oldFile = file with coordinates of the SNPs >> newFile = output file,) >> >> But this did not work. >> >> My oldFile was a .gff file as follows, >> >> Chrm Coordi alli old rs >> >> chr10 56397 C CT rs12262442 28 C/T 17 11 >> chr10 61776 T CT rs61838967 15 T/C 7 8 >>
Also, this doesn't appear to be gff, looks more like VCF. >> Was there a problem with my command line or with my .gff file ? ( or with >> both ?) >> >> Waiting for an early reply, >> >> Thank you very much. >> >> Anoma >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
