Optional Downstream Analysis Tools¶
Generate Protein Fasta¶
usage: pvacseq generate_protein_fasta [-h] [-d DOWNSTREAM_SEQUENCE_LENGTH]
input_file peptide_sequence_length
output_file
- Required Arguments
input_file A VEP-annotated single-sample VCF containing transcript, Wildtype protein sequence, and Downstream protein sequence information peptide_sequence_length Length of the peptide sequence to use when creating the FASTA. output_file The output fasta file - Optional Arguments
-d="1000", --downstream-sequence-length="1000" Cap to limit the downstream sequence length for frameshifts when creating the fasta file. Use ‘full’ to include the full downstream sequence. Default: 1000