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Hello all,
I am working on a neoantigene pipeline and using optitype for HLA detection. Optitype has an older FASTA version (2013) and the same alleles differ.
What is the assembly version of the …
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Hi,
When attempting to create a fresh bcbio install, I see the following:
```
Reading packages from /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/contrib…
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Hi,
I am using bcbio cancer germline and somatic mutation pipeline for my own exome data.
The config for my pipeline is
```
details:
- analysis: variant2
genome_build: GRCh37
# In order…
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Hello world, I am getting an error relating to the config files:
root@a1576648c921:/usr/local/bin/OptiType# /usr/local/bin/OptiType/OptiTypePipeline.py -i /data/cellline_chr21.fastq -d -o /data/out…
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## 0 packages
```
biopython==1.64
Coopr 3.5.8787 (CPython 2.7.6 on Linux 3.13.0-37-generic)
matplotlib==1.3.1
pandas==0.13.1
solver: glpk 4.35
```
## 1 run the example command on Ubuntu 14.04 LTS
``…
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Hello,
I'm getting several errors (below) when running joint VC with Strelka2 in bcbio-nextgen v.1.1.3 (stable). HaplotypeCaller works fine on my input data.
It also looks like Platypus isn't be…
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Hi
I have downloaded a few TCGA chr6 bam files which after converting them to fastq I've run in Optitype (docker version). I've used WXS and RNA for the available sample types (normal tissue, norma…
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Hi, I am using optitype for HLA typing, thanks for developing such a wonderful tool!
I firstly use razers3 and samtools to extract the reads mapped to hla genes(zero step), and then use OptiTypePipel…
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I'm running Optitype in docker. Is there any way to keep the aligned bam to reference HLA fasta? I think its created as intermediate file, and I would like to keep it.
Not sure how to modify the co…
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Hi,
I'm running optitype in rna mode for fastq.gz files. I get a large cryptic error that I'm not really able to figure out. Can someone help me translate this? See the command and error below:
…
ghost updated
6 years ago