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Run the test data as the flowing:
**step1**
python main_netMHCpan_pipe.py --preponly -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n TestRun -c 1 2 -E 8 9 10
INFO: Annovar r…
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Hello
I have some .vcf files but I don't have access to raw sequencing data or any patient specific HLA typing
I want to predict neoantigen load for my patients (of proving mutation burden)
I…
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Hello
I had run your software on my data wrongly put `c 1 2 parameter ` instead of `c 1` while my vcf files are single region so I have a results like
 from patients who have responded to chemotherapy versus a set of patients who have not responded.
I want to quantify the neoantigen load in the tumors ,can…
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Hi，all
I have tested about 30 samples for MHC-II type. They all worked well, but the result seemed quite different with that of MHC-I. The MHC_II neoantigens.Indels.txt was as following:
xq009…
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#### What analysis module should be updated and why?
PBTA vs TCGA TMB analysis In the works by @cansavvy #548 based on #551 and/or #257
#### What changes need to be made? Please provide enoug…
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Hello.
As far as I can understand - the main reason for using your own [netmhccons_1_1_python_interface.py](netmhccons_1_1_python_interface.py) are these lines:
```
#process_status_code = p.wai…
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Hello NeoPredPipe developers:
I am using the latest version of NeoPredPipe. I cloned the repo two days ago.
I am using Python 2.7.15 and I am on a Linux box
(Linux version 3.10.0-862.14.4.el…
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Hello,
I understand that MANTIS was designed to analyze DNA-based sequencing data, but I'm wondering if RNAseq bam files could be used as input data. Or is there any recommended software for estima…
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**Describe the bug**
neoantigen cases 1581, 1582, 1583 have wrong P length in .ali file.
Instead of 10, the peptide length is 9.
**Environment:**
alembick
**To Reproduce**
Steps/commands to …