Optional Downstream Analysis Tools

Generate Protein Fasta

usage: pvacseq generate_protein_fasta [-h] [-d DOWNSTREAM_SEQUENCE_LENGTH]
                                      input_file peptide_sequence_length

Positional Arguments

input_file A VEP-annotated single-sample VCF containing transcript, Wildtype protein sequence, and Downstream protein sequence information
 Length of the peptide sequence to use when creating the FASTA.
output_file The output fasta file

Named Arguments

-d, –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

Default: “1000”