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Implement a method of summarizing the variation inside of a graph.
* Drop out small, uncorrelated variation as noise while preserving correlated variation and building them into haplotype blocks.
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Elevated mutation rates at CpG dinucleotides are one of the major contributors to mutation rate variation in mammals. These can't easily be simulated by `sim_mutations`, but there are probably reasona…
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Hello Benjamin,
I've merged sequence tables of several `dada()` runs (in summary around 680 samples) and I am running the `collapseNoMismatch()` right now and it takes quite a while (it's running f…
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--Hello,
i have running Control-FREEC on a single chromosome with those parameters:
freec -conf config_WGS.txt
############# config_WGS.txt ###################
[general]
##parameters chrLen…
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### Need
As a clinician I want to be able to detect variants to a low allele frequency, as cheaply as possible, and with as few false positives as possible.
Using Sentieon Dedup from the new ve…
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The names of these make it unclear which type of entity each is meant to refer to. Based on child terms of the latter, I'm guessing that it refers to the actual molecules and the former refers to the …
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Hi,
Sorry for spamming the issues. I am having an error come up whenever I try to add a whitelist.
essentially the run report gives me no additional explanation other than:
failed: 11 at run…
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As visualization is not straightforward we strongly feel that it needs prototyping. Thus, we have decided to implement it as plugin for IGV.
We need to make some architectural decisions, so we need y…
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VR needs to have a path for representing translocations.
Allele is currently defined as a contiguous sequence change at a single location. Translocations and junctions are unlikely to fit in that m…
reece updated
4 months ago