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

Valerie Obenchain vobencha at fhcrc.org
Mon Dec 9 21:07:34 CET 2013

Hi Thomas,

On 12/08/2013 09:08 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

The variantReport() and codingReport() functions looks great. Would you 
be willing to contribute them to VariantAnnotation?

> (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.

I could add a 'REFLOC' column to the otuput of locateVariants() that 
would essentially be the "equivalent" to 'CDSLOC' from predictCoding().


> 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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Valerie Obenchain

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: vobencha at fhcrc.org
Phone:  (206) 667-3158
Fax:    (206) 667-1319

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