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Hello, I am working with VCF data called with GATK using hg19.
Now, when using VEP, I use the Grch37 reference (number 174), as they should be identical minus the MT genes.
I run VEP with the foll…
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Hi there,
I am trying to call neoepitopes using a locally installed version of topiary and NetMHCpan, and keep running into this error
> Traceback (most recent call last):
> File "/usr/loca…
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working directory: `/gscmnt/gc2547/griffithlab/yafeng/PRAD`
command: `pvacfuse run --net-chop-method cterm --netmhc-stab --iedb-install-directory /gscmnt/gc2502/griffithlab/yafeng -e 8,9,10,11 TCGA…
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i'm running pvacseq from pvactools 1.0.0 and run into the CSQ error
[EVL31-EVL54.vep.chr3.vcf.zip](https://github.com/griffithlab/pVACtools/files/1714017/EVL31-EVL54.vep.chr3.vcf.zip)
```
VC…
kylec updated
6 years ago
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Hi.
I've run pvacseq previously for a test and it wen't ok. Now I'm trying to do it for good but there is something that I'm not being able to understand.
By default I've python 2.7, so I use co…
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Hi, I came accorss an error on using netMHC through mhctools 1.6.5.
It works well with NetMHCpan and MHCflurry, with the fillowing commands
```
>>> from mhctools import NetMHCpan
>>> from mhctoo…
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See e.g.
https://bio.tools/tool/NetMHCpan/version/2.8
Many other examples
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I'm noticing that the temp fasta file is empty - some issue producing that?
Command: `bsub pvacfuse run --net-chop-method cterm --netmhc-stab --iedb-install-directory /gscmnt/gc2502/griffithlab/yaf…
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Ran the README example (with small edit as curly-braces are wrong currently)
Log lines:
```
INFO:root:netMHCpan -xls -xlsfile /tmp/netMHCpan_outputnbiuow68 -l 9 -f /tmp/peptideoog0vb52 -a HLA-A01:0…
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NetMHCIIpan v3.0 has several differences in its interface that require a separate class and output parser:
- no "-list" command
- no tmp directory option
- warnings with length = 20
- multiple tables …