[Bioc-devel] InteractionSet for structural variants

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 at 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 <seandavi at gmail.com> wrote:

On Tue, May 21, 2019 at 2:54 AM Aaron Lun <
infinite.monkeys.with.keyboards at 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 escribi?:

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

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Michael Lawrence

Scientist, Bioinformatics and Computational Biology

Genentech <https://www.gene.com/>, A Member of the Roche Group

Office +1 (650) 225-7760

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