Annovar

[Rez]

How can I add additional annotations like the gwas db or omim db to the output of summarize_annovar.pl either as an option for that script or after the output is already generated? Either way, I want these databases added to my annotated variant list from the summarize_annovar.pl script.

Any help would be much appreciated.

Thanks,

Nathan

After annotating your data by summarize-annovar.pl which would generate several temporal files and one file with all the annotations -(which is probablely called Genome...)- if you want to add more data to it, move the chr, strat, end, ref., alter. columns to the 1st,2,3,4 and 5th columns respectively and run this command:
perl annotate_variation.pl -filter -dbtype <omim/any-database> <your-file> humandb/

[Rez]

not to change the topic but snpEFF works quite awesome too

Annovar is more powerfull than SNPeff and Seattleseq.

[sheenams]

Annovar support email

The annovar support email (according to my cached version of the annovar page):

[email protected]

[Cable]

I have heard about snpEFF...I think I will try that one out too...thanks.

Edge: I cannot recall the email for Annovar supprt. As far as downloading, I did download all the databases into my humandb folder and annotated using the summarize_annovar script. There are additional databases I want to add to the output file of summarize_annovar and that is what I was asking about.

[adaptivegenome]

not to change the topic but snpEFF works quite awesome too

[edge]

Hi Cable,

Do you have the email address regarding help support of annovar website?
I plan to ask why can't access it since this morning
You just need to download all the database and save inside humandb.
I guess it should be able to work fiine...
Maybe you can explain more about your problem.
I will try to share with you if I know

[Cable]

Thanks, I used that script to download the databases. I just need to figure out how to put all those databases together.

The annovar website seems to be down right now. I just tried and it was unable to connect.

[edge]

I try and it work fine before with the following command:
eg

perl annotate_variation.pl -downdb -buildver hg19 hg19_phastConsElements46way.txt humandb/

I download one by one last time.
However I notice I can't access annovar website since this morning
Can you still access annovar website?

[Cable]

How can I add additional annotations like the gwas db or omim db to the output of summarize_annovar.pl either as an option for that script or after the output is already generated? Either way, I want these databases added to my annotated variant list from the summarize_annovar.pl script.

Any help would be much appreciated.

Thanks,

Nathan