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Dear all,
To my knowledge, I have installed OptiType and the required softwares and libraries, however I got the following error:
```
C02NQ30CG3QT:OptiType-master jimene01$ python OptiTypePipeline.…
SNRNS updated
8 years ago
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This is my first time running optitype, so forgive me if I missed something obvious. I am getting an odd parsing error. This also occurs with running the test dataset.
Command:
`python OptiTypePipe…
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Hi, I have been getting
```
Traceback (most recent call last):
File "/data/rozencompute2/a0073895/optitest/OptiType/OptiTypePipeline.py", line 304, in
"in your config file (currently %.3f), b…
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This is Yijia Li from Yunnan Province Stem Cell Bank, China.
We are very interested using your OptiType to do HLA typing.
However may I ask if I can use already mapped and SNP calling VCF to do that w…
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One of the samples not correctly predicted by OptiType is ERR031857, where A*02:06 is misclassified as A*02:01.
Even when expanding the results (`-e 5`), the correct solution is not found:
```
A…
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Hello again,
The OptiType paper says that "[OptiType] can be easily adapted to predict genotypes for loci other than HLA-I such as HLA-II". I was wondering if it's just a matter of changing some para…
SNRNS updated
8 years ago
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Should we also integrate wrapper function to prominent HLA typing methods?
Which one should those be besides OptiType?:
- seq2HLA
- Athlates
- HLAminer
- HLAforrest
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Hello!
I'm running into an error at the "Result dataframe has been constructed..." stage.
Here is he command I used:
`python ~/src/OptiType/OptiTypePipeline.py -v -i nebula_finished.fastq --dna -o .…
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Results after #1104 was fixed.
```
dwaggott@scg3-ln02: ~/ashley2/apps
$ rm -rf tmpbcbio-install
dwaggott@scg3-ln02: ~/ashley2/apps
$ bcbio_nextgen.py upgrade -u development --genomes hg38
Traceback …
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Hi,
I am trying to validate if bcbio is set right in our HPC. For this, we need a small data that can be optimised easily. That is why I would like to reproduce chr 6 data. When I run the process, th…