Version 4.3

Version 4.3.0

This is a minor feature release. It adds the following features:

• Add a new helper command pvacseq|pvacfuse|pvacbind|pvacvector valid_algorithms by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1108

• When running the pvacseq generate_protein_fasta command with the --phased-proximal-variants-vcf argument, output the intermediate proximal_variants.tsv file by @evelyn-schmidt in https://github.com/griffithlab/pVACtools/pull/1091

• In pVACview, clear the comment text input box after saving the comment by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1113

• Add support for mouse allele anchor positions by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1110

• Skip variants where VEP didn’t predict an amino acid change by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1121

• Update the ordering of the fasta file output of the pvacseq|pvacfuse generate_protein_fasta command when running with the --input-tsv argument so that the order of the fasta sequences is consistent with the order of the neoantigen candidates in the input TSV by @mhoang22 in https://github.com/griffithlab/pVACtools/pull/1002

• Updat the pvacfuse generate_protein_fasta command to allow aggregated TSVs as an input TSV by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1134

• Update pVACview to display the anchor positions currently applied to the data by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1114

This release also fixes the following bug(s):

• Handle invalid pVACfuse characters by trimming the sequence instead of skipping it. The previous implementation would lead to missing sequences in certain downstream steps, resulting in errors. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1130

• Add new pVACview R files to the list of files getting copied into the pVACseq output folder. These files were previsouly not copied in the the results folder, leading to error when running the pvacview run commands on a pVACseq output directory. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1126

• Remove single DP and DQ alpha and beta chain alleles from the list of supported alleles in MHCnuggetsII. This is because those alleles need to be defined as a pair of alpha- and beta-chains in order to be meaningful. Also remove DRA alleles from the same list since the DR locus is defined only by the beta chain because functional variation in mature DRA gene products is absent. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1133

• Fix errors in the rounding of the min and max values of the sliders in the custom pVACview module by @evelyn-schmidt in https://github.com/griffithlab/pVACtools/pull/1116

• Remove unused code in the Frameshift.pm VEP plugin that causes errors with certain types of variants by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1122