[Genome] use liftOver to update SNP postions?

[Ann Zweig]

Hello Yueming,

	Yes, the liftOver tool should work fine to map SNPs from mouse Build 36 (mm8) 
to Build 37 (mm9).  I would suggest that you get the mm8 coordinate positions of 
the SNPs you are interested in by using the Table Browser.

Table Browser User's Guide: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

	If you set up the filters and then restrict the output to only the chrom, 
chromStart, chromEnd and name fields, you will end up with a BED file that can 
be easily read by the liftOver tool.  Like so:

#chrom	chromStart	chromEnd	name
chr12	57628160	57628161	rs29205579
chr12	57628230	57628231	rs29211117
chr12	57628357	57628358	rs29193493
chr12	57628412	57628413	rs29222836

	You can feed that into the liftOver tool to map those SNPs (complete with their 
names) to the mm9 assembly.  If you would then like to view those mapped SNPs in 
the mm9 browser, you can make a custom track.

Custom Track User's Guide: http://genome.ucsc.edu/goldenPath/help/customTrack.html


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Yueming Ding wrote:
> 
> -----Original Message-----
> Hi Ann,
> 
> Do you think if I can use liftOver to get Build 37 positions for mouse SNPs (mapped on Build 36)?  Thanks.
> 
> Yueming Ding
> The Jackson Laboratory
>