[BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation

[Wei Shi]

Thanks Thomas, I have updated the biocViews terms for Rsubread to make it easier to be found.

Best regards,
Wei

On Dec 9, 2013, at 3:47 PM, Thomas Girke wrote:

> Thanks Wei for pointing this out, and sorry for missing this important
> utility. I will definitely give your exactSNP function a try. Associating 
> Rsubread with the biocViews term "GeneticVariability" (or similar) would 
> help users finding it in the future.
> 
> Thanks,
> 
> Thomas
> 
> On Mon, Dec 09, 2013 at 02:12:23AM +0000, Wei Shi wrote:
>> I just want to point out that Rsubread package includes a snp calling function called exactSNP.
>> 
>> Wei
>> 
>> On Dec 9, 2013, at 4:08 AM, Thomas Girke wrote:
>> 
>>> Dear Michael and Valerie,
>>> 
>>> VariantTools and VariantAnnotation are awesome packages. To the best of my
>>> knowledge, VariantTools is currently the only Bioc/R package that performs
>>> variant calling and it does this in a very nice way. With the available
>>> resources it is now straightforward to set up complete workflows for variant
>>> calling projects: (1) variant aware read alignments with GSNAP from gmapR ->
>>> (2) variant calling/filtering with VariantTools -> (3) adding genomic context
>>> with VariantAnnotation. This is really amazing!!! 
>>> 
>>> Here are a few questions related to both packages:
>>> 
>>> (1) For teaching purposes and other obvious reasons it would be useful if a
>>> Windows version of VariantTools were available (and perhaps for gmapR too).
>>> Installing the package (includes gmapR) from source works fine on both Linux
>>> and OS X, but not on Windows. 
>>> 
>>> (2) The VRanges class is another great resource for filtering variant calls.
>>> What I was not able to locate though is a description/definition of the content
>>> of its different columns/components. Is something like this available
>>> somewhere? 
>>> 
>>> (3) When annotation variants with utilities from VariantAnnotation, it would
>>> useful to provide a convenience Summary Report function at the end of the
>>> workflow that exports the annotations to a file. A very common need here is to
>>> collapse the annotations for each variant on a single line so that one doesn't
>>> end up with annotation results of millions of lines as it is typical for many
>>> variant discovery projects. This also simplifies joins among different
>>> annotation instances because it maintains uniqueness among variant identifiers.
>>> This approach is often useful when comparing (joining) the variants among
>>> different genotypes (e.g. which variants are identical or unique among
>>> different mutants). An example solution is shown on slides 34-35 of this
>>> presentation:
>>> http://faculty.ucr.edu/~tgirke/HTML_Presentations/Manuals/Workshop_Dec_12_16_2013/Rvarseq/Rvarseq.pdf
>>> 
>>> (4) predictCoding() reports the relative location where exactly a variant maps
>>> to an annotation range. It would be nice if locateVariants() could report the
>>> exact relative mapping locations too, e.g. variant chr1:1033_A/T maps to
>>> position x of 5'UTR. Perhaps this is already possible but I couldn't figure
>>> out how to do it without reaching too far into my own hacking toolbox.
>>> 
>>> Thanks for providing these excellent resources and most importantly your patience 
>>> listing to these unsolicited questions.
>>> 
>>> Best,
>>> 
>>> 
>>> Thomas
>>> 
>>> 
>>> 
>>>> sessionInfo()
>>> R version 3.0.2 (2013-09-25)
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>> 
>>> other attached packages:
>>> [1] VariantTools_1.4.5      VariantAnnotation_1.8.7 Rsamtools_1.14.2
>>> [4] Biostrings_2.30.1       GenomicRanges_1.14.3    XVector_0.2.0
>>> [7] IRanges_1.20.6          BiocGenerics_0.8.0
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] AnnotationDbi_1.24.0   BatchJobs_1.1-1135     BBmisc_1.4
>>> [4] Biobase_2.22.0         BiocParallel_0.4.1     biomaRt_2.18.0
>>> [7] bitops_1.0-6           brew_1.0-6             BSgenome_1.30.0
>>> [10] codetools_0.2-8        DBI_0.2-7              digest_0.6.3
>>> [13] fail_1.2               foreach_1.4.1          GenomicFeatures_1.14.2
>>> [16] gmapR_1.4.2            grid_3.0.2             iterators_1.0.6
>>> [19] lattice_0.20-24        Matrix_1.1-0           plyr_1.8
>>> [22] RCurl_1.95-4.1         RSQLite_0.11.4         rtracklayer_1.22.0
>>> [25] sendmailR_1.1-2        stats4_3.0.2           tools_3.0.2
>>> [28] XML_3.95-0.2           zlibbioc_1.8.0
>>> 
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>> 
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