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
