could pvactools be used for prediction in mice ?

[zhangyafeng1]

• pvactools version: 1.5.4 my pvactools version is 1.5.4 , and I found in the article that NetMHCpan 4.0 predict peptides to any MHC molecule 。 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6714459/ In pvactools version: 1.5.4 ， NetMHCpan version is 4.0 .
  So , could I use pvactools to predict in mice?

[susannasiebert]

Yes, you can use pVACtools to make predictions for mice but the available alleles are very limited:

$ pvacseq valid_alleles | grep H2
H2-IAb
H2-IAd
H2-IEd
$ pvacseq valid_alleles | grep H-2
H-2-Db
H-2-Dd
H-2-Kb
H-2-Kd
H-2-Kk
H-2-Ld

[malachig]

Fortunately, if you are working with common lab mice (as most people are) there is a good chance it will involve one of these alleles. e.g.

C57BL/6 is: H-2-Kb, H-2-Db, H2-IAb 129 is: H-2-Kb, H-2-Db, H2-IAb BALB/Cj is: H-2-Kd, H-2-Dd, H-2-Ld, H2-IAd, H2-IEd

http://tools.thermofisher.com/content/sfs/brochures/Mouse_Haplotype_Table.pdf http://jackson.jax.org/rs/444-BUH-304/images/MHC_h2_haplotypes.pdf

[zhangyafeng1]

Tkank you very much! but when I tested it, I met with some errors. My command line are as follows

pvacseq run \ MC38_somatic_final.vcf.gz \ MC38_Met_Lines \ H-2-Kb,H-2-Db \ NetMHCpan \ /out_dir/snv_pvac \ -e 8 \ -t 2 \ -p MC38_Met_Lines_phased_vep.vcf.gz \ --iedb-install-directory database_dir/mhc_database \ --normal-sample-name MC38_N_Lines

when it running Top Score Filter , the following error occurred , I didn't met this problem when I used a species human.

`Running Transcript Support Level Filter Complete Running Top Score Filter usage: pvacseq [-h] {run,binding_filter,coverage_filter,transcript_support_level_filter,top_score_filter,generate_protein_fasta,generate_condensed_ranked_report,download_example_data,install_vep_plugin,valid_alleles,allele_specific_cutoffs} ...

positional arguments: {run,binding_filter,coverage_filter,transcript_support_level_filter,top_score_filter,generate_protein_fasta,generate_condensed_ranked_report,download_example_data,install_vep_plugin,valid_alleles,allele_specific_cutoffs} run Runs the pVACseq pipeline binding_filter Filters variants processed by IEDB by binding score coverage_filter Filters variants processed by IEDB by coverage, vaf, and gene expression transcript_support_level_filter Filters variants processed by IEDB by transcript support level top_score_filter Pick the best neoepitope for each variant generate_protein_fasta Generate an annotated fasta file from a VCF with protein sequences of mutations and matching wildtypes generate_condensed_ranked_report Generate a condensed, ranked report from a pVACseq .all_epitopes.tsv or .filtered.tsv report file. download_example_data Downloads example input and output files install_vep_plugin Installs the Wildtype VEP plugin into your VEP_plugins directory valid_alleles Shows a list of valid allele names allele_specific_cutoffs Show the allele specific cutoffs

optional arguments: -h, --help show this help message and exit Error: No command specified Traceback (most recent call last): File "/ifs/TJPROJ3/HWEU/PUBLIC/software/reseq/pvac_python3/anaconda3/bin/pvacseq", line 8, in sys.exit(main()) File "/ifs/TJPROJ3/HWEU/USER/zhangyafeng/sorftware/anaconda3/lib/python3.7/site-packages/tools/pvacseq/main.py", line 92, in main args[0].func.main(args[1]) File "/ifs/TJPROJ3/HWEU/USER/zhangyafeng/sorftware/anaconda3/lib/python3.7/site-packages/tools/pvacseq/run.py", line 164, in main pipeline.execute() File "/ifs/TJPROJ3/HWEU/USER/zhangyafeng/sorftware/anaconda3/lib/python3.7/site-packages/lib/pipeline.py", line 469, in execute PostProcessor(**post_processing_params).execute() File "/ifs/TJPROJ3/HWEU/USER/zhangyafeng/sorftware/anaconda3/lib/python3.7/site-packages/lib/post_processor.py", line 33, in execute self.execute_top_score_filter() File "/ifs/TJPROJ3/HWEU/USER/zhangyafeng/sorftware/anaconda3/lib/python3.7/site-packages/lib/post_processor.py", line 102, in execute_top_score_filter TopScoreFilter(self.transcript_support_level_filter_fh.name, self.top_score_filter_fh.name, self.top_score_metric, self.file_type).execute() File "/ifs/TJPROJ3/HWEU/USER/zhangyafeng/sorftware/anaconda3/lib/python3.7/site-packages/lib/top_score_filter.py", line 82, in execute lowest_transcript_id = re.compile('ENST(\d+)').match(line_with_lowest_transcript_id['Transcript']).group(1) AttributeError: 'NoneType' object has no attribute 'group' `

could you give me some help? Thank you!

[zhangyafeng1]

I carried out this step alone for testing.

pvacseq top_score_filter MC38_Met_Lines.all_epitopes.tsv out.tsv

When I modified the beginning of transcript in input file from ENSMUST to ENST . The normal execution of the script is over.

I have a little confused . Did I miss some necessary parameters?

[susannasiebert]

This looks like a bug. I will look into it further.

[susannasiebert]

This bug has been fixed in version 1.5.9.