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Steps I've taken:
1) Filter out MHC region from WGS BAM file
- samtools view -b subject1.bam chr6:29940260-33086201 > subject1.mhc.bam
2) Sort BAM file and extract pair reads as fastq files
- sa…
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Hi Brad,
I am working through the tumor/normal synthetic 3 Teaching example for bcbio-nextgen, but I am receiving an error from the OptiType HLA typing:
```
subprocess.CalledProcessError:` Comm…
ghost updated
7 years ago
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OptiType is crashing with the following error message from the log:
```
mapping with 8 threads...
0:00:59.80 Mapping PGDX3144N_HLA_filtered_fished.fastq to GEN reference...
0:03:48.28 Gene…
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Hi,
I wanted to understand better the 1st step of HLA typing using Optitype in bcbio i.e. aligning to hg38 to extract fastq reads in HLA regions.
Are you using bwa-mem to align to the reference fast…
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I tried to install bcbio_nextgen on 2 different macs and on a cluster. In each case, I always get the same error (described below), where the package age-metasv seems to be absent. However, I have alr…
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Since Matplotlib 1.5.1, I see a warning (twice) each time I instantiate a `FontManager()`:
``` python
In [2]: from matplotlib.font_manager import FontManager
In [3]: FontManager()
/Users/tom/minicon…
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Hello,
OptiType returned the following message while calling the module `model.py`:
```bash
Invalid option '-s'; try /group/bioinformatics/software/GLPK/4.61/bin/glpsol --help
ERROR: "[base]/…
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Looking at the commits, this might already be fixed. However, can we get a release so I can update the Bioconda package?
```
+ OptiTypePipeline.py --config /tmp/tmp.7tWxKjFp3A/tmp.giJXfvqJlQ/tmp.d…
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Hi Brad,
My bcbio run has been unable to proceed past a certain T-N paired sample at the prioritisation step, up to the generation of the manta tsv files. I checked the commands and can't find anyt…
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Im getting a error I haven't come across before.
Any Ideas?
sudo python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local --genomes GRCh37 --aligners bwa
Checking required depe…