Question: gnomAD and Bravo to download loss-of-function annotation
0
gravatar for Shicheng Guo
12 days ago by
Shicheng Guo7.1k
Shicheng Guo7.1k wrote:

Hi All,

I want to download the annotation of 'loss-of-function' annotation in gnomAD and Bravo database. However, it seem you can find these annotation when using web service. When you download the data-base, these annotation were not included in the files. Why? Any suggestion?

http://gnomad.broadinstitute.org/

https://bravo.sph.umich.edu/freeze3a/hg19/

Update: Problem solved. The annotation is actually existed in the download VCF files after 'VEP='

Thanks.

ADD COMMENTlink modified 11 days ago • written 12 days ago by Shicheng Guo7.1k

Is there any reason you cannot do this annotation yourself?

ADD REPLYlink written 12 days ago by WouterDeCoster34k

I tried different approaches. However, none of them could provide as comprehensive annotation as gnomAD annotation. They have the following categories.

start_lost
missense_variant
inframe_deletion
splice_donor_variant
splice_region_variant
frameshift_variant
inframe_insertion
stop_gained
splice_acceptor_variant
stop_lost
stop_retained_variant
ADD REPLYlink written 11 days ago by Shicheng Guo7.1k
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