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Hi,
I am getting the following error when I test the Cancer tumor normal example. I think there are two main errors
1> "Aligning lane 1_2014-08-13_dream-syn3 with bwa aligner cat: write error: Br…
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Hello!
Let me start by saying thank you for all your hard work on this incredibly important project! This is a fantastic initiative.
I am using bcbio for the first time and am using the `tumor-p…
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Hey,
I've used ensemble mutation calling to call mutations which appear in 2/5 individual callers. I'm now wanting to go back and re-call those which appear in 3/5, 4/5, 5/5, and 1/5. Is there a w…
ghost updated
7 years ago
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---
## Expected Behavior
This was a working WF at version 1.0.20170622090721, should execute to completion. I cleaned out `~/.local` then `pip install --user cwltool`
## Actual Behavior
F…
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Hi,
I have a bcbio installed with GRCH37. Now that I have a client who is intersted in mm10. I was trying to do python bcbio_nextgen.py upgrade --genomes mm10 and I ran into Import Error for single…
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Hi Brad,
I have some tumor-only exome-seq data without matched normal data. But I still intend to call their somatic mutations. I read the online guidelines. It mentions that
For tumor-only sample…
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Hi Brad,
I have a question: I have to rerun a tomor/normal paired variant calling project with a lower min_allele_fraction. I still have the work directory. Could you tell me what I should delete to …
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Hi,
I've been running the analysis with bcbio installed on EBS volume connected to a single c4.2xlarge AWS instance, here's the config file:
```
details:
- algorithm:
platform: illumina
…
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Hi,
When I used the ensemble method, I encountered the following error:
`CalledProcessError: Command 'set -o pipefail; bcftools reheader -h /home/test/sample/work/varscan/samplecall-annotated-he…
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Hey,
So I'm wanting to combine mutations from multiple callers and do ensemble calling, but I want to do so including all called variants, not only those which are flagged as 'PASS'. I used the fo…
ghost updated
7 years ago