Hi,
I am trying through the packages that's been suggested.
My sincere thankfulness for your guidance.

Thanks & regards,
Jayakumar S


On Thu, Sep 26, 2013 at 12:29 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 9/25/2013 3:45 PM, jayakumar sivalingam wrote:
>
>> Hello,
>> Please let me know about the bioconductor packages to be used for the
>> following things:
>>
>>
>>     1. Quality check of the whole genome raw data
>>     2. Alignment
>>     3. SNP identification
>>
>
> In addition there is VariantTools (Linux only)
>
>   http://bioconductor.org/**packages/release/bioc/html/**VariantTools.html<http://bioconductor.org/packages/release/bioc/html/VariantTools.html>
>
>      4. Annotation
>>
>
>   http://bioconductor.org/help/**workflows/variants/<http://bioconductor.org/help/workflows/variants/>
>
> also of interest
>
>   http://bioconductor.org/**packages/release/bioc/html/**
> AnnotationHub.html<http://bioconductor.org/packages/release/bioc/html/AnnotationHub.html>
>   http://bioconductor.org/help/**community/<http://bioconductor.org/help/community/>
>   http://bioconductor.org/help/**course-materials/2013/**SeattleMay2013/<http://bioconductor.org/help/course-materials/2013/SeattleMay2013/>
>
>
>
>> Also, please let me know how I can be able to practice the above things
>> with the example data and the system requirements for the same.
>>
>
> Many packages come with sample data sets; many vignettes and work flows
> are fully executable, look for the 'R script' on package help pages and
> package landing pages.
>
> Packages usually operate 'across platforms' and many do not have
> third-party software requirements, although there are exceptions; actual
> system resources (e.g., memory) used vary by package and problem.
>
> Martin
>
>
>
>> Thanks & regards,
>> Jai
>>
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>>
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>>
>>
>
> --
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>

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