Optional Downstream Analysis Tools¶

Generate Protein Fasta¶

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

Positional 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

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”