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Dear *,
after a chat with @wm75 , I would like to share my / our experiences within this issue.
I encountered several problems when I tried to run the [MIRACUM workflow](https://github.com/AG-Boer…
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I had a question regarding CNVkit's use of CBS as implemented by DNAcopy. I have been using DNAcopy in a workflow including VarScan's copynumber and copyCaller commands. The instructions for that tool…
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Hi,
I temporarily solved issue [#2838](https://github.com/bcbio/bcbio-nextgen/issues/2838) by adding `BCBIO_DIR` to my`PATH`. However, while this leads to successful execution of `dkfzbiasfilter`, …
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Hi,
Sorry for opening another issue. It looks like there is something wrong with either bcftools command or the header of scalpel vcf files:
```
Traceback (most recent call last):
File "/mnt/p…
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Hi Brad,
The latest template for paired tumor (https://github.com/bcbio/bcbio-nextgen/blob/master/config/templates/tumor-paired.yaml) uses vardict, mutect2 and strelka2. I wonder why freebayes or v…
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Hi brad,
This time I am trying to do our 3rd bcbio installation on aws ec2. I am getting the below error. can you please help?
ERROR conda.core.link:_execute(502): An error occurred while instal…
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Hello -
I am trying to run BCBIO 1.1.6 version on SLURM/Lustre file system. Many of my samples completed runs successfully with 3 different variant callers - Mutect2, Strelka2, Varscan and then cr…
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Hi,
I intended to get automatic snpeff and vep annotated exome-seq results and added
effects:
- snpeff
- vep
under the - algorithm: in the yaml file. However, the following error appeared i…
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Hi there,
I am doing a test about the function of VarScan (v2.4.3) fpfilter, but I am confused how to make the readcount region for insertions. For SNVs, the regions look like "chr pos pos", and th…
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I'm recently running PVACseq on a bunch of VEP-annotated germline variants vcf with netMHC, and some of the samples will show up an error of "Type names and field names must be valid identifiers" in C…