Hello Matt, The first entry in your BED input is the cause of the error you are seeing:
1 752566 752567 rs3094315 Should be: chr1 752566 752567 rs3094315 For more information on BED format please see this FAQ: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 6/6/12 2:36 PM, Matthew Kowgier wrote: > Dear all, > > I am attempting to convert a bed file that is in hg19 (build 37) coordinates > to hg18 (build 36) coordinates with the linux command line versions of > liftOver using the conversion file hg19ToHg18.over.chain.gz. I am getting the > following error for every line (or SNP) in my bed file: '#Deleted in new'. > > If it helps, here is an example of 3 lines from my bed file which I wish to > convert to hg18: > 1 752566 752567 rs3094315 > 1 776546 776547 rs12124819 > 1 846808 846809 rs4475691 > > The online liftOver utility also reports the same error message as the > command line version for these 3 lines: > > #Deleted in new > 1 752566 752567 rs3094315 > #Deleted in new > 1 776546 776547 rs12124819 > #Deleted in new > 1 846808 846809 rs4475691 > > > Why is liftOver not able to identify these SNPs? What am I doing wrong? > Any help would be appreciated. > > Many thanks, > Matt > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
