Comments (4)
Hi,
do you mind sharing/mailing the following files, so that I can check what happens:
/XXX/work/89/b85145dc36f106bca16fa3f0c7007d/PB-16-002_vep_somatic_gx.vcf.gz
/XXX/work/89/b85145dc36f106bca16fa3f0c7007d/PB-16-002_peptides.fasta
/XXX/work/89/b85145dc36f106bca16fa3f0c7007d/PB-16-002_mixMHC2pred.tsv
/XXX/work/89/b85145dc36f106bca16fa3f0c7007d/PB-16-002_mixMHC2pred.tsv
Thanks
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Sure, see zipped folder, please let me know if you prefer me to send it by email.
Thank you a lot
SV
[Archive.zip](https://gith
Archive.zip
ub.com/icbi-lab/nextNEOpi/files/9243596/Archive.zip)
from nextneopi.
Thanks for reporting this issue.
There seem to occur rare situations where VEP can not assign a gene symbol to annotate a mutation, this caused the problem with our mixMHC2pred
parser.
I fixed the problem now and made a new release.
You may also just download the fixed parser script from https://github.com/icbi-lab/nextNEOpi/raw/master/bin/parse_mixMHC2pred.py and place it into your nextNEOpi
bin
directory and resume the pipeline with the -resume
command line option.
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