SNP effect prediction

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SNP effect prediction

Pablo Cingolani
  I had to predict the effect of a few thousand SNP that we found in
our re-sequencing project. I tried
using ENSEMBL's tool
(http://www.ensembl.org/Homo_sapiens/UserData/UploadVariations), but
it was kind of
painful (it only admits 700 SNPs, takes a long time, etc.).

  So I decided to write a java program (snpEff). I noticed that Galaxy
does not have a tool for SNP prediction
(see http://bitbucket.org/galaxy/galaxy-central/issue/156/synonymous-and-non-synonymous-snps).
So I integrated
snpEff it with Galaxy.

  Here is a link to a tar file which includes the jar files,
databases, configuration files for Galaxy, etc.

      http://www.mcb.mcgill.ca/~pcingola/snpEff.tgz

   YOu'll find the databases for hg37 and mm37, but I'll be happy to
create and update the tool for
the genome of your choice. The program first loads the database for a
genome (it takes 20 secs in my
computer) and then calculates the effect for all SNPs (I used an
Interval-Tree structure, so it's very fast).

  I hope you find it useful.
  Yours

     Pablo Cingolani


P.S.: Needless to say, the code is open source (I'll post it on
sourceforge as soon as possible). In the mean time
you can download it here
http://www.mcb.mcgill.ca/~pcingola/SnpEffect_eclipse_project.tgz

P.S.2: I've attached an image of a demo run in my Galaxy server

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Re: SNP effect prediction

Anton Nekrutenko
Pablo:

Please upload your new tool to our new community site http://usegalaxy.org/community

Thank you very much for contributing!!!

anton
galaxy team


On Jul 5, 2010, at 10:38 PM, Pablo Cingolani wrote:

>  I had to predict the effect of a few thousand SNP that we found in
> our re-sequencing project. I tried
> using ENSEMBL's tool
> (http://www.ensembl.org/Homo_sapiens/UserData/UploadVariations), but
> it was kind of
> painful (it only admits 700 SNPs, takes a long time, etc.).
>
>  So I decided to write a java program (snpEff). I noticed that Galaxy
> does not have a tool for SNP prediction
> (see http://bitbucket.org/galaxy/galaxy-central/issue/156/synonymous-and-non-synonymous-snps).
> So I integrated
> snpEff it with Galaxy.
>
>  Here is a link to a tar file which includes the jar files,
> databases, configuration files for Galaxy, etc.
>
>      http://www.mcb.mcgill.ca/~pcingola/snpEff.tgz
>
>   YOu'll find the databases for hg37 and mm37, but I'll be happy to
> create and update the tool for
> the genome of your choice. The program first loads the database for a
> genome (it takes 20 secs in my
> computer) and then calculates the effect for all SNPs (I used an
> Interval-Tree structure, so it's very fast).
>
>  I hope you find it useful.
>  Yours
>
>     Pablo Cingolani
>
>
> P.S.: Needless to say, the code is open source (I'll post it on
> sourceforge as soon as possible). In the mean time
> you can download it here
> http://www.mcb.mcgill.ca/~pcingola/SnpEffect_eclipse_project.tgz
>
> P.S.2: I've attached an image of a demo run in my Galaxy server
> <Galaxy_SnpEff.png>_______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev

Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org




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Re: SNP effect prediction

Pablo Cingolani
Done. Please let me know if everything is in the right format.
Yours
    Pablo

P.S.: Keep in mind that the tool has to read the database (it takes 20
secs) before start processing the SNPs.

On Tue, Jul 6, 2010 at 8:26 AM, Anton Nekrutenko <[hidden email]> wrote:

> Pablo:
>
> Please upload your new tool to our new community site http://usegalaxy.org/community
>
> Thank you very much for contributing!!!
>
> anton
> galaxy team
>
>
> On Jul 5, 2010, at 10:38 PM, Pablo Cingolani wrote:
>
>>  I had to predict the effect of a few thousand SNP that we found in
>> our re-sequencing project. I tried
>> using ENSEMBL's tool
>> (http://www.ensembl.org/Homo_sapiens/UserData/UploadVariations), but
>> it was kind of
>> painful (it only admits 700 SNPs, takes a long time, etc.).
>>
>>  So I decided to write a java program (snpEff). I noticed that Galaxy
>> does not have a tool for SNP prediction
>> (see http://bitbucket.org/galaxy/galaxy-central/issue/156/synonymous-and-non-synonymous-snps).
>> So I integrated
>> snpEff it with Galaxy.
>>
>>  Here is a link to a tar file which includes the jar files,
>> databases, configuration files for Galaxy, etc.
>>
>>      http://www.mcb.mcgill.ca/~pcingola/snpEff.tgz
>>
>>   YOu'll find the databases for hg37 and mm37, but I'll be happy to
>> create and update the tool for
>> the genome of your choice. The program first loads the database for a
>> genome (it takes 20 secs in my
>> computer) and then calculates the effect for all SNPs (I used an
>> Interval-Tree structure, so it's very fast).
>>
>>  I hope you find it useful.
>>  Yours
>>
>>     Pablo Cingolani
>>
>>
>> P.S.: Needless to say, the code is open source (I'll post it on
>> sourceforge as soon as possible). In the mean time
>> you can download it here
>> http://www.mcb.mcgill.ca/~pcingola/SnpEffect_eclipse_project.tgz
>>
>> P.S.2: I've attached an image of a demo run in my Galaxy server
>> <Galaxy_SnpEff.png>_______________________________________________
>> galaxy-dev mailing list
>> [hidden email]
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> Anton Nekrutenko
> http://nekrut.bx.psu.edu
> http://usegalaxy.org
>
>
>
>

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