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**Is your feature request related to a problem? Please describe.**
We need to create a minimal germline variant calling pipeline use case setup here
- https://github.com/bihealth/snappy-use-case-g…
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I am implementing this microtest repository and am wondering what should be placed in the [data path] section in these code blocks:
required_input_files: [data_path]
ngs_input_files: [data…
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Hi,
I recently ran the epic2-df example but got an error.
Below is the output:
$ epic2-df -fdrc 1 -tk /home/user/anaconda3/lib/python3.8/site-packages/epic2/examples/test.bed.gz -tw /home/u…
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Hello :)
I have a question regarding viral-ngs and its capabilities for detecting virus integration and outputting the results to a text file. I tried to understand the explanation provided in the …
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Hi,
I've been trying to compare some variant calling methods to use on mitochondria NGS data.
I've seen that you test your pipeline with HG00119 and I was wondering if you had curated a set of hig…
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## **Describe the bug**
I've been looking at how the pipeline runs, and I noticed something strange. I'm doing something pretty simple, just running chip-seq analysis of existing data on a new refere…
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Exception thrown on pipeline launch, seems to be a Caper problem (get same output when running caper without input JSON). Running on SLURM cluster with pipeline v1.8.0.
**Caper configuration file**…
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Related #204
So today they filled their hard drive while running the pipeline.
The fastq files they are running are very large since they only ran 12 or 24 samples in the run.
An example project th…
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run sequenza on sample = SJRHB011_Y_T4D_E_EGAS00001002528
Processing chr1: 1681 variant calls; 3834 heterozygous positions; 287402 homozygous positions.
Processing chr2: 1107 variant calls; 3166 heter…
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Hi,
I am using this pipeline to reanalyze some data from Illumina Novaseq PE250bp.
And I have noticed that in this paper , they sequenced at Hiseq PE250bp (McNichol, J., Berube, P., Biller, S.…