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
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
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