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**Is your feature request related to a problem? Please describe.**
We need to create a minimal cancer variant calling pipeline use case setup here
- https://github.com/bihealth/snappy-use-case-can…
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I'm using the example data from the documentation.
In v1.6.0 - the file `chr20.germline.vcf` does not get generated from the germline calling step.
```
${path}/src/Monopogen.py germline -a ${pa…
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The current readme contains information that hasn't been tested with the current rbFlowLite version. It needs to be updated once everything has been verified to work satisfactorily on TSD.
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Hi, I am running Germline, after successfully running preProcess.
I met a few problems.
First, when I ran germline, the output showed that I didn't have Java. So, I installed Java using `conda inst…
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Hi @arahuja @ryan-williams ,
Sorry for deviating you from your work. Could you please look into the issue am facing with.
I looked into htsjdk version 1.118 there are several new…
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When I run prepocess.py with a sorted bam file, the following error occurs after some time: ValueError: fetch called on a bam file without index. How do I fix it?
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### Description of feature
Could be good to do whatever can be done when we release to help prepare for validation.
I'm thinking benchmarking, GiAB, checking results...
Could be interesting to talk…
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Dear Eric et al,
I have been trying to produce a precomputed Canvas .binned file from a panel of normals for the purpose of calling germline CNVs in future. Whilst I have been able to generate the…
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The germline WES workflow specifically should be limited to regions of interest in the form of an input interval_list. I believe the interval_list is already an input, but:
A) the interval_list shoul…
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Hi Brad,
I am assuming the recall jar uses optimized parameter settings for the variant caller based on bcbio settings. I've been looking at exploring incremental join calling on tumour only samples.…