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Hello,
I'm getting intermittent errors when running tests with 100 small FASTQ files on an SGE cluster using Cromwell. The jobs are sometimes able to finish fine, but more often than not (4 out of …
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I wanted to run CNVkit call with VarScan somatic variants to get LOH, however it skipped all my variants:
> Selected test sample TUMOR and control sample NORMAL
> Loaded 0 records; skipped: 198662…
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Hi,
I got the following error when running SomaticSeq train with the following command:
```
singularity exec /groups/zuber/zubarchive/USERS/tobias/.singularity/somaticseq:3.0.0.img \
/opt/soma…
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VAFs are another output of the detect_variants workflow that are currently missing. These can be calculated from bam-readcount output, see #127. However, annotating the VCF with new VAFs has been a lo…
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I generated CWL using `bcbio_vm.py cwl` and attempted to run the resulting workflow with `cromwell`. Things progressed until the pipeline tried to run varscan as seen here: https://github.com/bcbio/b…
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Hi Christoffer,
Here is an unexpected question for you :P
As I understand it, superFreq uses the reference normal samples for two purposes:
a) To calculate the differential coverage over captu…
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Hello,
I would like to try SMuRF to predict variants from BAM.
Here what I run on test files.
myresults
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## SNV pipeline
- [x] Mutect2 pipeline - *done*
- [x] VarScan2
Optional
- LoFreq (for tumor-only or ones with low VAF)
@sbamin can you provide callers you used for canine and a link to t…
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I was running Variant calling for normal/tumor samples using bcbio with 4 variant callers.
If I understood right, there is some problem with one of the last steps, merging vcf files:
[2018-10-27T1…
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Hi. I am trying to run the pipeline, but keep getting this error despite adding Picard to the path (CLASSPATH) as suggested. Please help.
I have fulfilled all dependencies, and surprisingly Varsca…