-
Hi Dave and Feiyu,
Just wanted to note that the latest CLE somatic results do not seem to be reporting the most severe consequence in the variants.annotated.tsv. I only noticed this being an iss…
-
## Bug Report
I'm trying to create JSON from [this CWL](https://github.com/ga4gh/dockstore/files/694312/varscan_cwl.txt).
This works:
`cwltool --non-strict --print-pre varscan.cwl > test.json`
A…
-
Hello lima,
When I use PureCN with a vcf produced by other variant calling software other than Mutect2,
I got this error below, whether it's because the vcf format is not fit, what critical inform…
-
This is my config file:
`details:
- algorithm:
tools_off:
- tumoronly-prioritization
- gemini
- coverage_qc
aligner: bwa
trim_reads: true
mark_duplicates: …
-
Just did a clean install of bcbio followed by upgrade to latest-devel and ran the cancermulti test and had that fail.
```[2019-09-16T17:13Z] tabix index PairedBatch-effects-annotated-damage-ann-noe…
-
Hello, we are using VEP in GDC-like pipeline after VarScan step.
This is our VEP launch command:
`/soft/ensembl-vep-95/vep --fork 14 --input_file Test.all.all.hc.fp-filtered-D3.Somatic.vcf --format …
-
Hello,
I am using the following command to call the variants. My intention here is to speed up this process while retaining all the variant information that is needed.
```
samtools mpileup
…
-
Hi,
I ran 15 samples to use delly2.
but only 2 samples stoped and I got error message like this;
[2019-Apr-29 19:19:53] SV annotation
0% 10 20 30 40 50 60 70 80 90 100%
|-…
-
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`, …
-
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…