I know little about SV and the associated software, but it is clear to me that we will see a lot of "personal" genomes in the future and having the ability to move between different reference genomes (coordinate systems) will be something I think we should think about having good/great support for.
On Tue, May 21, 2019 at 9:37 AM Michael Lawrence via Bioc-devel < bioc-devel@r-project.org> wrote: > The new package StructuralVariantAnnotation is worth mentioning. It > operates on the general "breakend" notation so should be able to represent > any type of structural variant. > > On Tue, May 21, 2019 at 3:22 AM Sean Davis <seand...@gmail.com> wrote: > > > On Tue, May 21, 2019 at 2:54 AM Aaron Lun < > > infinite.monkeys.with.keyboa...@gmail.com> wrote: > > > > > > Thanks for your response. So far my intention is to to plot them and > I > > > > do not intend on performing any other operation. The first step would > > be > > > > read in the VCF file and transform it into a meaningful object and I > > was > > > > hoping there was a core package already taking care of that, but I > get > > > > from your answer that there's no such functionality implemented. > > > > > > Not to my knowledge... but if you're planning on writing some relevant > > > functions, I'm sure we could find a home for it somewhere. > > > > > > > I do have a couple of simple functions in VCFWrenchR (not in Bioc), but > > like much VCF code, it probably misses a bunch of edge cases. The > functions > > target VRanges, not interactionsets. > > > > https://github.com/seandavi/VCFWrenchR > > > > Sean > > > > > > > -A > > > > > > > El 5/18/19 a las 4:47 AM, Aaron Lun escribió: > > > >> I would say that it depends on what operations you intend to perform > > > >> on them. You can _store_ things any way you like, but the trick is > to > > > >> ensure that operations and manipulations on those things are > > > >> consistent and meaningful. It is not obvious that there are > meaningful > > > >> common operations that one might want to apply to all structural > > > >> variants. > > > >> > > > >> For example, translocations involve two genomic regions (i.e., the > two > > > >> bits that get stuck together) and so are inherently > two-dimensional. A > > > >> lot of useful operations will be truly translocation-specific, e.g., > > > >> calculation of distances between anchor regions, identification of > > > >> bounding boxes in two-dimensional space. These operations will be > > > >> meaningless to 1-dimensional variants on the linear genome, e.g., > > > >> CNVs, inversions. The converse also applies where operations on the > > > >> linear genome have no single equivalent in the two-dimensional case. > > > >> > > > >> So, I would be inclined to store them separately. If you must keep > > > >> them in one object, just lump them into a List with "translocation" > > > >> (GInteractions), "cnv" (GRanges) and "inversion" (another GRanges) > > > >> elements, and people/programs can pull out bits and pieces as > needed. > > > >> > > > >> -A > > > >> > > > >> > > > >> On 5/17/19 4:38 AM, Bernat Gel Moreno wrote: > > > >>> Hi all, > > > >>> > > > >>> Is there any standard recommended container for genomic structural > > > >>> variants? I think InteractionSet would work fine for translocation > > and > > > >>> GRanges for inversions and copy number changes, but I don't know > what > > > >>> would be the recommended way to store them all together using > > standard > > > >>> Bioconductor objects. > > > >>> > > > >>> And actually, is there any package that would load a SV VCF by > lumpy > > or > > > >>> delly and build that object? > > > >>> > > > >>> Thanks! > > > >>> > > > >>> Bernat > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > -- > > Michael Lawrence > > Scientist, Bioinformatics and Computational Biology > > Genentech <https://www.gene.com/>, A Member of the Roche Group > > Office +1 (650) 225-7760 > > micha...@gene.com <lastname.firstname-or-u...@gene.com> > > > Join Genentech on LinkedIn <https://www.linkedin.com/company/genentech> | > Twitter > < > https://twitter.com/genentech?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor > > > | Facebook <https://www.facebook.com/Genentech/> | Instagram > <https://www.instagram.com/genentech/?hl=en> | YouTube > <https://www.youtube.com/genentech> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
