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Old 10-03-2010, 09:49 AM   #3
Location: USA

Join Date: Oct 2009
Posts: 41

Originally Posted by svl View Post
One option (but perhaps not the most complete) is to use the Ensembl SnpEffectPredictor script:

There is also an online version (mirror site, because their main site is down):

Both will annotate your variants (eg chr:1 123456 A/T) with their effect (eg NON_SYNONYMOUS, but also SPLICE_SITE and ESSENTIAL_SPLICE_SITE)

This is the list with types it will return:

Thanks! Do you know if there is any script or online tool that can deal with data downloaded from UCSC? I am concerned with the possible conflict of the format or coordinate between ensembel and UCSC.
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