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Old 11-26-2011, 05:32 AM   #1
moty
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Location: Israel

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Default Variation analysis - tool recommendation

Hi all,
I need to analyze some variation I detected using GATK's UnifiedGenotyper.
(if this is of any relevance, I am using hg19 as reference)
So, basically I have this .vcf file and I want to screen out variation that aren't in any known genes for starters. after doing my share of reading I stumbled upon ANNOVAR, BEAGLE, SIFT, VariantClassifier and more.
does anyone have a favorite of his own? or maybe can recommend a method for achieving what I'm after?

Thanks to all the helpers
Moty
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Old 11-28-2011, 01:56 AM   #2
Bukowski
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Quote:
Originally Posted by moty View Post
Hi all,
I need to analyze some variation I detected using GATK's UnifiedGenotyper.
(if this is of any relevance, I am using hg19 as reference)
So, basically I have this .vcf file and I want to screen out variation that aren't in any known genes for starters. after doing my share of reading I stumbled upon ANNOVAR, BEAGLE, SIFT, VariantClassifier and more.
does anyone have a favorite of his own? or maybe can recommend a method for achieving what I'm after?

Thanks to all the helpers
Moty
I like the ENSEMBL VEP:

http://www.ensembl.org/info/docs/variation/vep/

not least because it wraps up functional and positional annotations into a single interface, but it has web based and API based access, and a handy Perl script to do the heavy lifting if you so desire.
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Old 11-28-2011, 02:28 AM   #3
NGSfan
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Does VEP require online access or can it be run locally?

I am behind a firewall and it does not always give me access to everything.
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Old 11-28-2011, 02:39 AM   #4
Bukowski
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Quote:
Originally Posted by NGSfan View Post
Does VEP require online access or can it be run locally?

I am behind a firewall and it does not always give me access to everything.
We run a local installation, mirroring the required parts of Ensembl.
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Old 11-28-2011, 02:40 AM   #5
cjp
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You can install the EnsEMBL database on a local Linux machine and get the API to see that, but am not sure if the VEP can be made to work on a local machine. The best place to ask is the mailing list:

http://lists.ensembl.org/mailman/listinfo/dev

Chris
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Old 11-28-2011, 05:52 AM   #6
NGSfan
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Thanks Bukowski and cjp for the information and suggestions. I am using ANNOVAR and I'm really quite happy with it, but have always been curious about the VEP. I just hesitate because I get the impression that there is a lot of overhead in using the VEP compared to ANNOVAR if one wants to run it locally.
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