-
Dear Sigve,
I just update my local ```cpsr``` analysis pipeline to the latest version. However, an error message popped up when I used the example vcf file, and the same error message popped up whe…
jxshi updated
4 years ago
-
I have 75 affected individuals and I tried to variant call all of them together placing them in the same batch. This yielded a final VCF file for all samples.
From a previous study, I know for sur…
-
**Version info**
- bcbio-nextgen==1.2.4
- Ubuntu 20.04.1 LTS
**To Reproduce**
Exact bcbio command you have used:
```
sudo apt-get -y update
sudo apt-get -y install aptitude
sudo DEBIAN_FRO…
-
**Version info**
- bcbio version 1.2.3
Hi guys,
I am trying to add the "--max-mnp-distance 0" command to mutect2 for building a PON database. I have not managed to get it to include this param…
waemm updated
4 years ago
-
Hello, everyone!
Not exactly a bcbio issue, but a situation which is hard to catch when calling and prioritizing germline variants with bcbio/vep/vcfanno/gemini.
When using vep annotations and v…
-
I've trying to install and test using the AshekanziTrio reference from here ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio
I keep getting stalled at the annotation step for various r…
-
Hello, bcbio developers and users!
Thanks for the great pipeline!
I've read in the history that it is now possible to use vcfanno in RNA-seq analysis.
When trying this:
```
details:
- algori…
-
https://github.com/hammerlab/vcf-annotate-polyphen/blob/efcf086ec537075d4677f539af4c1c4dcdfbcdad/vap/cli.py#L52
Can we patch this to the above line
```python
'chr{}'.format(v.CHROM.replace('chr…
-
**Version info**
- bcbio version (bcbio_nextgen.py --version): 1.2.3
- OS name and version: Ubuntu 18.04 bionic
**To Reproduce**
- Exact bcbio command you have used
> bcbio_nextgen.py -t l…
-
Dear Bcbio team,
We installed bcbio new version v1.2.0 & tried to run gatk-variant pipeline. It is giving the below error.
We tried adding tools_on: gemini to yaml file. Still It is giving errors…