Optional Downstream Analysis Tools

Generate Protein Fasta

usage: pvacseq generate_protein_fasta [-h] [--input-tsv INPUT_TSV]
                                      [-p PHASED_PROXIMAL_VARIANTS_VCF]
                                      [--mutant-only]
                                      [-d DOWNSTREAM_SEQUENCE_LENGTH]
                                      [-s SAMPLE_NAME]
                                      input_vcf flanking_sequence_length
                                      output_file

Generate an annotated fasta file from a VCF with protein sequences of
mutations and matching wildtypes

positional arguments:
  input_vcf             A VEP-annotated single- or multi-sample VCF containing
                        genotype, transcript, Wildtype protein sequence, and
                        Downstream protein sequence information.The VCF may be
                        gzipped (requires tabix index).
  flanking_sequence_length
                        Number of amino acids to add on each side of the
                        mutation when creating the FASTA.
  output_file           The output fasta file.

optional arguments:
  -h, --help            show this help message and exit
  --input-tsv INPUT_TSV
                        A pVACseq all_epitopes or filtered TSV file with
                        epitopes to use for subsetting the input VCF to
                        peptides of interest. Only the peptide sequences for
                        the epitopes in the TSV will be used when creating the
                        FASTA. (default: None)
  -p PHASED_PROXIMAL_VARIANTS_VCF, --phased-proximal-variants-vcf PHASED_PROXIMAL_VARIANTS_VCF
                        A VCF with phased proximal variant information to
                        incorporate into the predicted fasta sequences. Must
                        be gzipped and tabix indexed. (default: None)
  --mutant-only         Only output mutant peptide sequences (default: False)
  -d DOWNSTREAM_SEQUENCE_LENGTH, --downstream-sequence-length DOWNSTREAM_SEQUENCE_LENGTH
                        Cap to limit the downstream sequence length for
                        frameshifts when creating the fasta file. Use 'full'
                        to include the full downstream sequence. (default:
                        1000)
  -s SAMPLE_NAME, --sample-name SAMPLE_NAME
                        The name of the sample being processed. Required when
                        processing a multi-sample VCF and must be a sample ID
                        in the input VCF #CHROM header line. (default: None)

This tool will extract protein sequences surrounding supported protein altering variants in an input VCF file. One use case for this tool is to help select long peptides that contain short neoepitope candidates. For example, if pvacseq was run to predict nonamers (9-mers) that are good binders and the user wishes to select long peptide (e.g. 24-mer) sequences that contain the nonamer for synthesis or encoding in a DNA vector. The protein sequence extracted will correspond to the transcript sequence used in the annotated VCF. The alteration in the VCF (e.g. a somtic missense SNV) will be centered in the protein sequence returned (if possible). If the variant is near the beginning or end of the CDS, it will be as close to center as possible while returning the desired protein sequence length. If the variant causes a frameshift, the full downstream protein sequence will be returned unless the user specifies otherwise as described above.

Generate Aggregated Report

usage: pvacseq generate_aggregated_report [-h] input_file output_file

Generate an aggregated report from a pVACseq .all_epitopes.tsv report file.

positional arguments:
  input_file   A pVACseq .all_epitopes.tsv report file
  output_file  The file path to write the aggregated report tsv to

optional arguments:
  -h, --help   show this help message and exit

This tool produces an aggregated version of the all_epitopes TSV. It finds the best-scoring (lowest binding affinity) epitope for each variant, and outputs additional binding affinity, expression, and coverage information for that epitope. It also gives information about the total number of well-scoring epitopes for each variant, the number of transcripts covered by those epitopes, as well as the HLA alleles that those epitopes are well-binding to. Lastly, the report will bin variants into tiers that offer suggestions as to the suitability of variants for use in vaccines. For a full definition of these tiers, see the pVACseq output file documentation.