.. image:: ../images/pVACseq_logo_trans-bg_sm_v4b.png
    :align: right
    :alt: pVACseq logo

.. _optional_downstream_analysis_tools_label:

Optional Downstream Analysis Tools
==================================

Generate Protein Fasta
----------------------

.. program-output:: pvacseq generate_protein_fasta -h

.. .. argparse::
    :module: lib.generate_protein_fasta
    :func: define_parser
    :prog: pvacseq generate_protein_fasta

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
--------------------------

.. program-output:: pvacseq generate_aggregated_report -h

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 :ref:`output file documentation <aggregated>`.