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Old 08-08-2012, 03:04 PM   #1
Cable
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Default Annovar

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
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Old 08-13-2012, 09:27 PM   #2
edge
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I try and it work fine before with the following command:
eg
Code:
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?
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Old 08-13-2012, 09:57 PM   #3
Cable
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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.
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Old 08-14-2012, 05:02 AM   #4
edge
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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
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Old 08-14-2012, 05:40 AM   #5
adaptivegenome
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not to change the topic but snpEFF works quite awesome too
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Old 08-14-2012, 11:53 PM   #6
Cable
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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.
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Old 08-15-2012, 12:38 PM   #7
sheenams
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Default Annovar support email

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

kai@openbioinformatics.org
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Old 10-24-2012, 01:26 PM   #8
Rez
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Wink

Quote:
Originally Posted by adaptivegenome View Post
not to change the topic but snpEFF works quite awesome too
Annovar is more powerfull than SNPeff and Seattleseq.
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Old 10-24-2012, 01:44 PM   #9
Rez
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Quote:
Originally Posted by Cable View Post
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/

Last edited by Rez; 10-24-2012 at 01:49 PM.
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