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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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Reporting 2 runs with different inputs and different failures:
1)
I first tried pVACvector with a list of the best peptide per variant from my pVACseq results, which contained 24 peptides. It erro…
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Hi I ran the following command and got errors, does anybody know what might be wrong?
```
pvacseq run $root_dir/pvacseq_example_data/input.vcf Test HLA-A*02:01,HLA-B*35:01,DRB1*11:01 NetMHCIIpan Net…
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How to install previous versions of pvactools. I think the current version may conflict with the machine I am using. When I execute the command pvacseq run -h, the terminal does not display anything.
41526 updated
5 years ago
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First My vcf is annotated by VEP in docker and my command:
./vep -i /opt/vep/.vep/maf2vcf/ACC-US-t.vcf --offline --format vcf --symbol --terms SO --vcf --plugin Downstream --plugin Wildtype -o /op…
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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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Added from https://github.com/griffithlab/pVAC-Seq/issues/342
Original requestor: @sashakotov2
My problem is that several pvacseq runs were with this error:
![pvacseq_error](https://user-image…
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So netmhciipan takes DQ and DP alleles in the following format:
HLA-DPA10401-DPB19901
HLA-DQA10101-DQB10201
It would be great if mhctools could take an mhcfile with 2 DQA1 alleles and 2 DQB1 alleles…
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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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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 …