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
>
> 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
_______________________________________________
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