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I'm attempting to write a bam file of the realigned reads, as I'm seeing ADs in the vcf that do not line up with what is present in the input bam file. I'm mainly concerned with two specific locations…
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plugin version: 0.95-2020.3
### Description
I have a problem after update to the specified version in WebStorm IDE.
Editor window does not accept keyboard input, and the `Analyzing...` label is…
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When comparing FreeBayes (v0.9.21-19-gc003c1e) NA12878 indels with the NIST gold standard, I found a pattern among the false negatives (FNs).
The first 6 FN indels I looked at mainly were at homopol…
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For all centos cluster admins go to the last entry for install instructions.
Dear Developers of octopus
We got a request from a user of our cluster system to make octopus available as a module…
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Hi,
I am trying to borrow some of the code from deepvariants, specifically importing realigner. What is the best way to do this?
Thank you
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Hello,
I am using abra2 as intel realigner in my workflow after alignment with bwa and before variant calling with freebayes. It works quite nicely, until now. In my most recent run, the workflow cra…
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### Short description
When a Lombok dependency is present, the warning is still there.
### Expected behavior
The warning to not be displayed. (Or even consider [whether the warning is useful …
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I am comparing several BAM files from different aligner programs using same data. Surprisingly, I cannot ensure all tracks are sorted using readnames. Each aligner ended up with diiferent number of re…
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Hello, I am trying to install DeepVariant on an IBM Power 8 machine within a docker container.
I get the following error during ./build_and_test.sh, which I understand is tied to Intel SSE2 instruc…
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Hi Brent,
First of all, thanks for hts-nim!
I'm writing a realigner using hts-nim. For the realignment I have a seq[CigarElement] but am struggling to convert that to Cigar. newCigar() takes a p…