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Hi,
I am having problems running Sarek with the latest version of nextflow (19.07). The error I get is:
```
Command error:
.command.run: line 196: uname: command not found
.command.run: l…
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Hi
I recently installed docker version of deep variant for cancer exome analysis. I like to know if I don't use paired cancer samples for variant calling with deep variant will it be right approac…
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Posting issue on @cmnbroad's request.
I see this stacktrace of a WARN for some GATK tools. The tools proceed to run successfully. For example, LearnReadOrientationModel gives this. I've been prepa…
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Brad,
The other day I was looking at WES data of different read length and evaluated the performance of GATK4 and freebayes using NA12878. When doing a series of analyses with data trimmed to diffe…
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During the upload phase for step 5, I am running into an error with VEP while it attempts to run the file. Below are the steps I took to run the command and the second blurb is where the error shows u…
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Hi, I'm using version 1.6.0 and I was hoping that running the `var2vcf_paired.pl` script with the `-M` flag (used to output only candidate somatic variants) would filter out variants marked with `STAT…
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The `germlineVcfBedPe` channel will include duplicates when the same normal is used in more than one tumor-normal pairing within the same run. This results in a file name collision error.
https://g…
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Hi @sigven ,
Thank for your cpsr and pcgr software. I have used pcgr for a while and I love it. I tried cpsr today and successfully tested the example ```vcf``` file. When I tried to use my own dat…
jxshi updated
5 years ago
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I Brad, thanks for implementing purecn. I am trying this in some target panel and in case there when there are few or no mutation it fail. There is a way to catch this?
Thnanks!
Alessandro
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I just downloaded the docker image and ran the following test on Centos OS 7. Everything worked fine.
INPUT_DIR="/test/DeepVariant/quickstart-testdata"
OUTPUT_DIR="/test/Deep…