This is confusing the SV calling with the issue of moving between
coordinate systems which exists even with great/perfect genomes. Good point
on deletions and the new system, but it is nevertheless important
People do this for example for some of the new mouse genomes using modmap.
On Tue, May 21
We're never going to have great support for genome coordinate systems for
SV due to the intrinsic complexity involved. Even something as simple as a
deletion is problematic if the coordinate system change results in
additional sequence in the deleted region (is that also deleted or not?),
or some o
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.
The single package builder should be back online and available utilizing Bioc
3.10 devel builders.
Thank you for your patience.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
___
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 wrote:
> On Tue, May 21, 2019 at 2:54 AM Aaron Lun <
> infinite.monkeys.with.k
>And actually, is there any package that would load a SV VCF by lumpy or
delly and build that object?
It sounds like you're looking for my StructuralVariantAnnotation package.
It's designed to load SV calls in any of various representations supported
by VCF (direct REF/ALT sequence differences, sy
Hi Steffen,
Thanks for your response. I want to do something useful by extending other BioC
packages through S4 classes, essentially looking for documentation and
mentoring. I will have more details next week.
Best,
Patrick Casimir, PhD
C: 954.614.1178
-Original Message-
From: Neuman
Hello maintainers,
Now that the devel builds have been stable for a few weeks we will transition
the single package builder to also be building off Bioc 3.10. The transition
will begin this morning and hopefully only last a few hours. During this period
the Single Package Builder will be off
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 mea
