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I used annovar to annotate variants with 1kg european frequecny and exac NFE frequncy.
I found out that many of the variants the exist in the 1kg DB don't appear in the Exac DB.
From what i red, i und…
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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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Hi All,
Collecting some information and opinions around RNA-seq variant calling here. The Broad institute have released best practices for germline variant calling in RNA-seq, http://gatkforums.broadi…
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Dear bpipe,
I'm trying to run an example in the "Running Pipeline Stages in Parallel", but it doesn't appear to work. I'm using the bpipe-0.9.9 release on a Mac.
Firstly, the "nice_to_see_you" stage…
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Hello,
I used GATK to analyze a gene panel for several subjects. I used snpEff for annotation and then used GATK's variantannotator to make the final vcf file. Now when I am trying to make a GDS f…
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Tool ids should be unique and meaningful. We need them to reference tools in a several places. There are tools with whitespaces inside of tool id's, like EMBOSS or tools with case sensitive id's.
We …
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The PGX app does not really rely on annotations except for the inclusion of rsID's. which should be included during the actual forming of the vcf file. Is it worth annotating the files and offering th…
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Extra Variant Annotation
At the moment, we are essentially throwing out any non annovar annotation, this can have the side effect of losing a lot of information. Should this data be kept?
Processing …
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I'm calling bpipe like this:
```
bpipe run -n 8 -m 14GB ../minc-bpipe-library/pipeline.bpipe
```
The bpipe log file looks like:
```
10 bpipe.Config [1] INFO |7:11:39 Merging pipeli…
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After uploading 3 WGS variant call filles the server appeared to crash. The issues appears that somewhere there is blocking code stopping the server performing properly. It is unable to send and recei…