griffithlab/pVACtools

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• Investigate possible utility of TCRbridge (AlphaBridge, Alphafold3)

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1470 · Opened Sep 25, 2026

• Interpreting junction scores in pVACvector.

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1468 · 1 comment · Opened Sep 21, 2026

• Update pVACcompare list of valid columns

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  bug report / hotfix PR

  Difficulty 3/5 1-2 days Newbie friendliness 58/100

  griffithlab/pVACtools#1465 · Opened Sep 17, 2026

• pVACseq should handle frameshift that fall "within the region of the splice site"

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  Difficulty 4/5 3-5 days Newbie friendliness 55/100

  griffithlab/pVACtools#1464 · Opened Sep 14, 2026

• Don't use special characters in tmp file names

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  Difficulty 2/5 1-3 hours Newbie friendliness 72/100

  griffithlab/pVACtools#1455 · Opened Aug 24, 2026

• add support for ctat-lr-fusion expression

  May be free again @mhoang22 claimed this 55 days ago, and no pull request is open. Open

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  feature addition

  griffithlab/pVACtools#1450 · 1 assignee · Opened Aug 11, 2026

• Does pvacseq run support custom HLA/MHC sequencing input via NetMHCpan's -hlaseq option for non-model organisms?

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  Difficulty 5/5 Over a week Newbie friendliness 35/100

  griffithlab/pVACtools#1415 · Opened Jul 6, 2026

• Consider new stability prediction algorithm SPEARMINT

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1413 · Opened Jul 1, 2026

• Add AA -> mRNA backtranslation to pVACvector

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  Difficulty 5/5 Over a week Newbie friendliness 35/100

  griffithlab/pVACtools#1411 · Opened Jun 16, 2026

• Proposal: staged behavior-preserving refactor of tool responsibility placement

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1408 · 3 comments · Opened Jun 6, 2026

• Update IEDB to use Next-Generation (NG) IEDB Tools API

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  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  griffithlab/pVACtools#1400 · Opened May 21, 2026

• Add NMD prediction support

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1370 · 1 reaction · Opened Mar 6, 2026

• Suggestion to use WhatsHap for phasing VCFs

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  griffithlab/pVACtools#1362 · 2 comments · 1 reaction · Opened Jan 22, 2026

• Investigate AEGIS for class II prediction

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  prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1361 · Opened Jan 16, 2026

• Investigate MARIA for class II predictions

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  prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1360 · Opened Jan 16, 2026

• Use tumor ploidy and cellularity estimates from FACETS and/or Sequenza for clonality assessment

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  feature addition

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1355 · 1 comment · Opened Jan 5, 2026

• TypeError: a bytes-like object is required, not 'NoneType'

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  bug report / hotfix PR

  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  griffithlab/pVACtools#1347 · 13 comments · Opened Dec 9, 2025

• Investigate adding pMHCchat as an additional binding prediction tool

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  prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1269 · Opened Jul 15, 2025

• Add a command to create a colored ordering TXT/DOC file for DNA vectors

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  Difficulty 5/5 Over a week Newbie friendliness 35/100

  griffithlab/pVACtools#1251 · Opened Jun 18, 2025

• Running pVACSeq on multiple samples

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  Difficulty 5/5 Over a week Newbie friendliness 20/100

  griffithlab/pVACtools#1246 · 13 comments · Opened Jun 3, 2025

• Incorporate gene of interest status in the aggregate tiering/sorting

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  Difficulty 5/5 Over a week Newbie friendliness 30/100

  griffithlab/pVACtools#1230 · Opened Apr 9, 2025

• investigate TLimmuno2

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  prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1205 · Opened Feb 18, 2025

• Console warnings/errors

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  bug report / hotfix PR pVACview

  Difficulty 4/5 3-5 days Newbie friendliness 25/100

  griffithlab/pVACtools#1199 · Opened Feb 7, 2025

• Consider HLApollo for integration

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  grant prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 20/100

  griffithlab/pVACtools#1172 · Opened Jan 6, 2025

• Plans for adding NetTCR-2.0?

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  prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1141 · 1 comment · Opened Sep 7, 2024

• Potential improvements to the pVACview NeoFox module

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  pVACview

  Difficulty 5/5 Over a week Newbie friendliness 20/100

  griffithlab/pVACtools#1098 · Opened Apr 30, 2024

• Output a visual representation of the graph after all spacers have been tested

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  pVACvector

  Difficulty 5/5 Over a week Newbie friendliness 30/100

  griffithlab/pVACtools#1089 · 1 comment · Opened Apr 5, 2024

• QUESTION: How to integrate netchop results to aditionnally filter possible peptides

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  griffithlab/pVACtools#1064 · Opened Feb 19, 2024

• Overview of possible new prediction algorithms and their installation/run requirements

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  prediction_algorithms

  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  griffithlab/pVACtools#1056 · 2 comments · Opened Jan 26, 2024

• Consider integration with ACE a tool for generation of ELISpot configurations (peptide-pool assignments)

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  prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1051 · Opened Jan 16, 2024

• Investigate DeepHLApan prediction algorithm

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  grant prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#1016 · Opened Aug 9, 2023

• Evaluate MHCRank for integration

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  prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 20/100

  griffithlab/pVACtools#1007 · Opened Jul 24, 2023

• Add matched WT to pVACfuse predictions

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  grant

  Difficulty 5/5 Over a week Newbie friendliness 35/100

  griffithlab/pVACtools#993 · Opened Jul 6, 2023

• Investigate Pepsickle as an alternative to NetChop

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  prediction_algorithms

  Difficulty 4/5 3-5 days Newbie friendliness 25/100

  griffithlab/pVACtools#986 · Opened Jun 22, 2023

• Update reference proteome analysis to consider patient genotype

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  grant

  Difficulty 5/5 Over a week Newbie friendliness 30/100

  griffithlab/pVACtools#948 · 3 comments · Opened Apr 7, 2023

• Should anchor position be a criteria in the aggregate reprot for class II predictions?

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  Difficulty 5/5 Over a week Newbie friendliness 20/100

  griffithlab/pVACtools#940 · 1 comment · Opened Mar 29, 2023

• Implement a `--ignore-rna-in-tiering` flag

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  Difficulty 3/5 1-2 days Newbie friendliness 52/100

  griffithlab/pVACtools#910 · Opened Mar 6, 2023

• Incorporate better handling of HLA allele-specific expression loss

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  grant

  Difficulty 5/5 Over a week Newbie friendliness 20/100

  griffithlab/pVACtools#901 · Opened Feb 14, 2023

• Investigate adding support for EpiScan Predictor

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  grant prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#894 · Opened Jan 9, 2023

• Add support for screening of end modifications to long peptides to accommodate manufacture/solubility issues

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#880 · 2 comments · Opened Dec 6, 2022

• Add retry when NetMHCstabpan fails

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  Difficulty 3/5 1-2 days Newbie friendliness 45/100

  griffithlab/pVACtools#862 · Opened Oct 27, 2022

• Explore incorporation of "Inhibigens" in neoantigen candidate prioritization

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  grant

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#829 · 2 comments · Opened Jul 14, 2022

• Use MHCgnomes to help resolve HLA alleles

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#827 · Opened Jul 11, 2022

• pVACseq stability predictions are not performed locally with --netmhc-stab

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  griffithlab/pVACtools#791 · 1 comment · Opened Apr 4, 2022

• Add ability to run the reference proteome step on the full peptide sequence in a fasta

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  Difficulty 4/5 3-5 days Newbie friendliness 30/100

  griffithlab/pVACtools#787 · 2 comments · Opened Mar 22, 2022

• Incorporate DeepNeo for better class II priortization

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  grant prediction_algorithms

  Difficulty 5/5 Over a week Newbie friendliness 20/100

  griffithlab/pVACtools#777 · 2 comments · Opened Feb 22, 2022

• Add retry when calls to standalone IEDB fail

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  Difficulty 3/5 1-2 days Newbie friendliness 35/100

  griffithlab/pVACtools#762 · 10 comments · Opened Jan 25, 2022

• Add support for proximal inframe indels

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  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  griffithlab/pVACtools#757 · 1 comment · Opened Jan 19, 2022

• Incorporate predictions from TCRMatch

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  grant prediction_algorithms

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  griffithlab/pVACtools#755 · 1 comment · Opened Jan 17, 2022

• Consider use of APE-Gen algorithm

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  grant prediction_algorithms

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  griffithlab/pVACtools#709 · 2 comments · Opened Sep 22, 2021