How/ where can I download Annotation exac03(hg19) database and import it to Galaxy?

Dear Galaxy community,

I need to add EXAC_NFE info in VCF.
I am thinking about useing “SnpSIFT annotate” to annotate the SNP ID with EXAC_NFE as INFO.
However, I could not find a way to download the exac03(hg19) file and import it to Galaxy. (Tried already to find information from ANNOVAR, UCSC, and ExAC Browser, but could not find a way to get the file.)

Can anyone help me with that?
Or maybe I am wrong, it is not the way to add EXAC_NFE information.

Thanks a lot

Susan

Hi Susan,
the simplest way to bring in these annotations would be via the GEMINI toolsuite, just that
a) you’ll have to stop working with VCF format at that point because GEMINI converts VCF to an sqlite database during the annotation step and keeps using this format for all further processing and querying
b) with the current version of GEMINI, you’ll only have ExAC release 0.3 available
c) you would have to work on usegalaxy.eu for now because GEMINI, for technical reasons, is currently not available on usegalxy.org (though hopefully this will get fixed in the not so distant future)

If you want to try to annotate your VCF directly (SnpSift annotate may or may not work for the task - I never tried to use it for anything but dbSNP data) the data you’re looking for is available from:
ftp://ftp.broadinstitute.org/pub/ExAC_release

The files you find there have been compressed with bgzip, but if you specify data type “VCF” on import Galaxy should unpack them for you.

1 Like