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## For UI issues
* Tool: Varscan
* Version: [this one](https://github.com/chopdgd/bfx-tools-wdl/blob/develop/varscan/VarScan.wdl) (2.3.9)
### Description
This Varscan task only uses `mpileup2c…
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GIven the interest in studies that involve tumor heterogeneity / subclonality, currently bcbio offers "out of the box" support for both somatic variants and CNVs. A useful metric that can be combined …
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Hello.
Today I updated cwltool on my machine from cwltool-1.0.20190228155703 to latest cwltool-1.0.20190618201008.
After this update all my pipelines became broken.
As I discovered from starter log…
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Hello,
I tested different mincoverages (from 1 to 9) for two samples. Bizarrely, I detected more SNPs with higher coverages for the same input data and settings except for --mincov parameter. Is t…
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Dear developers,
on 18.09.2019 we upgraded to bcbio v1.1.6a0 (`devel` branch). When running a `variant2` analysis (with the exact same configuration that we extensively used across several WES runs…
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Hi,
I am having this issue when I try to run the example:
```R
myresults sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.10
Mat…
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Reads: /mnt/gpfs/Hackathon/AD7_Complete/cutadapt/
snurk updated
5 years ago
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Hello.
According to these lines in files: [somatic_exome.cwl#L13](https://github.com/genome/analysis-workflows/blob/master/definitions/pipelines/somatic_exome.cwl#L13), [detect_variants.cwl#L10](http…
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I am trying to perform ensemble variant analysis against GRCh37 with Freebayes, Varscan and VarDict. However, there seems to be a hold up on VarDict's inference:
```
[2017-04-05T15:38Z] Genotypin…
ghost updated
5 years ago
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Hi, Chase.
I have been trying to work with SNPGenie and can't figure out how to troubleshoot this error -- `CDS_EXAMPLE.gtf does not contain any sense (+) strand products. SNPGenie terminated.`.
…