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https://github.com/ChristofferFlensburg/superFreq/blob/dd98abd82c183b9faafacca9a244766ed2df3c24/R/runVariantAnnotation.R#L13
Hi Chris, I'm having some issues with the latest version (v1.5.1) in RNA…
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- [x] implement tumor-normal variant calling with DRAGEN
- [x] document for accreditation
- [ ] Also implent tumor-only calling with DRAGEN?!
- [x] Also add somatic SV calling with dragen?
- [x] test …
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Right now, the AMI seems to be missing a fair number of tools that will be needed for the course, mostly from pmbio lessons that will be used. Let's use this thread to organize those updates and make …
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**Is your feature request related to a problem? Please describe.**
Many wrappers are untested. This is not good. Writing tests for them *en bloc* will not work because of the sheer number. This must …
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### Checklist
- [X] I added a descriptive title
- [X] I searched open reports and couldn't find a duplicate
### What happened?
I updated the conda few days ago, then the conda seems not working, al…
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As needed by @QJohn2017 a setup script for tianhe2 is needed (see #89). Since tianhe2 uses SLURM for scheduling, either the `./prepare_job` script needs to be adjusted to an `./prepare_job_tianhe2.sh`…
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Hello,
The number of SNPs and the sum of transitions+transversions does not match in the snpEff CSV output. I ran snpEff on a sample called "B86097":
```
snpEff
-Xms750m
-csvStats B8…
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toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6
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Hi there; as a preface, I am very new to bioinformatics, but I have had some issues in running the slamdunk count / alleyoop utrrate commands. When I put the following into my terminal, all that happe…
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Hi,
I'm having a problem running PureCN, which seems to be a problem with the vcf file - I've attached this. This is a Varscan vcf, but I can't figure out what's wrong with it. The error references…