On Sun, Dec 8, 2013 at 9:08 AM, Thomas Girke <thomas.girke@ucr.edu> 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.
>
>
Julian has already helped answer some of these questions (thanks!). For
Windows support, I would need to talk to Tom about how far he could port
the GMAP suite. VariantTools currently relies on bam_tally, but I've also
written a simple function that generates a basic VRanges via
Rsamtools::applyPileups. It will become part of VariantAnnotation. Many
filters in VariantTools just rely on the basic read depth information, so I
could make gmapR a Suggested dependency of VariantTools, and thus allow
VariantTools to work on Windows. Tallying is a computationally intensive
operation, so I'm guessing Windows users would be using the downstream
functionality.

Also interesting would be integration of the HDF5 representation, i.e.,
input/output to/from VRanges and generation via applyPileups. Does that
already exist? And there's also the idea of storing the tallies as a
tab-separated file, with a Tabix index. The advantage is that it would rely
only on Rsamtools.

(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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