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Since #153 was added, we can now make use of an unsupervised method for filtering out variants. This would probably be done via a VQSR-like method. @andrewmchen is working on this, IIRC.
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`HaplotypeCaller` and `VQSR` are a two-pass team in which first we call variants permissively and then filter. There are several advantages of this approach:
- Rather than scattering filtration all o…
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Hi bcbio developers!
I have validated RNA-seq variant calling in BCBIO with SRR307898 dataset (GM12878 cell line).
The precision is 90%.
In bcbio-nextgen/bcbio/rnaseq/variation.py I see 3 steps
``…
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```
[2016-06-29T15:11Z] 9ed8b9305dd7: Finalizing variant calls: HG01977, freebayes
[2016-06-29T15:11Z] 9ed8b9305dd7: Calculating variation effects for HG01977, freebayes
[2016-06-29T15:11Z] 9ed8b9305d…
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Hi,
I would like to remove common dbsnp from my vcfs and thank you for setting up an tutorial for this case. However, during the removal of the dbsnp from the vcfs. I encountered with an error. My da…
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Hello,
I added the following tools to my Dockerfile:
```
RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o pjbriggs --name macs21 --panel-section-name NGS:_Peak_Calling_Youtube" \
"--…
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I'm thinking about implementation of products filtering. It should be definitely external package, for example as reaction-search. This functionality might be helpful on any page with list of products…
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As a user and as a shop administrator, I want to be able to search for products by tag/keyword across the whole store.
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Hello,
I tried to upload a VCF file (3.7 MB) which has caused _Failed: Bad Request (400)_ with the following Dockerfile:
```
FROM bgruening/galaxy-stable:dev
MAINTAINER auto script
ENV GALAXY_CONFIG_…
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The only thing that I lack in dgrid is filter plugin like in enhanced grid.