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**Some of the neaopeptide modelling were not finished successfully**
The _modeller.log_ complaining the alignment and PDB are not matched.
**On alembick:**
- Inputs:
case: _1083_ neopeptide
…
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Hello
Our cluster computing group has installed your software via docker on our server like below which directed me to R environment
```
module load singularity/3.2.1
singularity pull antigen.…
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* pvactools version: **docker://griffithlab/pvactools:1.5.9**
* Python version:
* Operating System:
**Describe the bug**
This is similar or identical to #571, where we hit [this exception](htt…
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I would like to use the ScanNeo pipeline and would like to reproduce the results described in the [paper](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz193/5384…
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Hello,
I'm running into an error with OptiType. I'm pasting the lines from the R.optitype.log file below:
0:00:01.97 Generating binary hit matrix.
Traceback (most recent call last):
File "/u…
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"""
**2. Single somatic MAF file**
• Includes all somatic mutations (point/indels) along with annotation, filtering, FACETS CCFs, neoantigen predictions (neo_* columns from somatic_variants/neoantig…
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Related to the following: https://hub.docker.com/r/cmopipeline/netmhc
https://github.com/mskcc/vaporware/pull/314
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Below two lines result in duplicated level of neoantigen directory in the "Result" folder when publishing the result
https://github.com/mskcc/vaporware/blob/bfc446dc16336802790e6644f37e1e9f0cc32fd8…
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We have planned to include an analysis of tumor mutation burden as well as a comparison to the tumor mutation burden of adult tumors in TCGA. This issue is for fleshing out the analysis. The manuscrip…
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pvactools version: 1.3.0
Python version: 3.5.5
Operating System: Linux
**Describe the bug**
`.filtered` file is empty even though there are plausible candidates in `.all_epitopes` file
**To R…