.. image:: ../images/pVACfuse_logo_trans-bg_sm_v4b.png :align: right :alt: pVACfuse logo Output Files ============ The pVACfuse pipeline will write its results in separate folders depending on which prediction algorithms were chosen: - ``MHC_Class_I``: for MHC class I prediction algorithms - ``MHC_Class_II``: for MHC class II prediction algorithms - ``combined``: If both MHC class I and MHC class II prediction algorithms were run, this folder combines the neoepitope predictions from both Each folder will contain the same list of output files (listed in the order created): .. list-table:: :header-rows: 1 * - File Name - Description * - ``.tsv`` - An intermediate file with variant and transcript information parsed from the input file(s). * - ``.tsv_`` (multiple) - The above file but split into smaller chunks for easier processing with IEDB. * - ``.fasta`` - A fasta file with mutant peptide subsequences for all processable fusion combinations. * - ``.all_epitopes.tsv`` - A list of all predicted epitopes and their binding affinity scores, with additional variant information from the ``.tsv``. * - ``.filtered.tsv`` - The above file after applying all filters, with cleavage site and stability predictions added. * - ``.filtered.tsv.reference_matches`` (optional) - A file outlining details of reference proteome matches * - ``.all_epitopes.aggregated.tsv`` - An aggregated version of the ``all_epitopes.tsv`` file that gives information about the best epitope for each mutation in an easy-to-read format. Filters applied to the filtered.tsv file ---------------------------------------- The filtered.tsv file is the all_epitopes file with the following filters applied (in order): - Binding Filter - Top Score Filter Please see the :ref:`Standalone Filter Commands` documentation for more information on each individual filter. The standalone filter commands may be useful to reproduce the filtering or to chose different filtering thresholds. all_epitopes.tsv and filtered.tsv Report Columns ------------------------------------------------ In order to keep the outputs consistent, pVACfuse uses the same output columns as pVACseq but some of the values will be ``NA`` if a column doesn't apply to pVACfuse. .. list-table:: :header-rows: 1 * - Column Name - Description * - ``Chromosome`` - The chromosome of the 5p and 3p portion of the fusion, separated by " / " * - ``Start`` - The start position of the 5p and 3p portion of the fusion, separated by " / " * - ``Stop`` - The stop position of the 5p and 3p portion of the fusion, separated by " / " * - ``Reference`` - ``fusion`` * - ``Variant`` - ``fusion`` * - ``Transcript`` - The Ensembl IDs of the affected transcripts * - ``Transcript Support Level`` - ``NA`` * - ``Ensembl Gene ID`` - ``NA`` * - ``Variant Type`` - The type of fusion. ``inframe_fusion`` for inframe fusions, ``frameshift_fusion`` for frameshift fusions * - ``Mutation`` - ``NA`` * - ``Protein Position`` - The position of the fusion in the fusion protein sequence * - ``Gene Name`` - The Ensembl gene names of the affected genes * - ``HGVSc`` - ``NA`` * - ``HGVSp`` - ``NA`` * - ``HLA Allele`` - The HLA allele for this prediction * - ``Peptide Length`` - The peptide length of the epitope * - ``Sub-peptide Position`` - The one-based position of the epitope in the protein sequence used to make the prediction * - ``Mutation Position`` - ``NA`` * - ``MT Epitope Seq`` - Mutant epitope sequence * - ``WT Epitope Seq`` - ``NA`` * - ``Best MT Score Method`` - Prediction algorithm with the lowest mutant ic50 binding affinity for this epitope * - ``Best MT Score`` - Lowest ic50 binding affinity of all prediction algorithms used * - ``Corresponding WT Score`` - ``NA`` * - ``Corresponding Fold Change`` - ``NA`` * - ``Best MT Percentile Method`` - Prediction algorithm with the lowest binding affinity percentile rank for this epitope * - ``Best MT Percentile`` - Lowest percentile rank of this epitope's ic50 binding affinity of all prediction algorithms used (those that provide percentile output) * - ``Corresponding WT Percentile`` - ``NA`` * - ``Tumor DNA Depth`` - ``NA`` * - ``Tumor DNA VAF`` - ``NA`` * - ``Tumor RNA Depth`` - ``NA`` * - ``Tumor RNA VAF`` - ``NA`` * - ``Normal Depth`` - ``NA`` * - ``Normal VAF`` - ``NA`` * - ``Gene Expression`` - ``NA`` * - ``Transcript Expression`` - ``NA`` * - ``Median MT Score`` - Median ic50 binding affinity of the mutant epitope of all prediction algorithms used * - ``Median WT Score`` - ``NA`` * - ``Median Fold Change`` - ``NA`` * - ``Median MT Percentile`` - Median binding affinity percentile rank of the mutant epitope across all prediction algorithms used (those that provide percentile output) * - ``Median WT Percentile`` - ``NA`` * - ``Individual Prediction Algorithm WT and MT Scores and Percentiles`` (multiple) - ic50 binding affintity and percentile ranks for the ``MT Epitope Seq`` for the individual prediction algorithms used * - ``cterm_7mer_gravy_score`` - Mean hydropathy of last 7 residues on the C-terminus of the peptide * - ``max_7mer_gravy_score`` - Max GRAVY score of any kmer in the amino acid sequence. Used to determine if there are any extremely hydrophobic regions within a longer amino acid sequence. * - ``difficult_n_terminal_residue`` (T/F) - Is N-terminal amino acid a Glutamine, Glutamic acid, or Cysteine? * - ``c_terminal_cysteine`` (T/F) - Is the C-terminal amino acid a Cysteine? * - ``c_terminal_proline`` (T/F) - Is the C-terminal amino acid a Proline? * - ``cysteine_count`` - Number of Cysteines in the amino acid sequence. Problematic because they can form disulfide bonds across distant parts of the peptide * - ``n_terminal_asparagine`` (T/F) - Is the N-terminal amino acid a Asparagine? * - ``asparagine_proline_bond_count`` - Number of Asparagine-Proline bonds. Problematic because they can spontaneously cleave the peptide * - ``Best Cleavage Position`` (optional) - Position of the highest predicted cleavage score * - ``Best Cleavage Score`` (optional) - Highest predicted cleavage score * - ``Cleavage Sites`` (optional) - List of all cleavage positions and their cleavage score * - ``Predicted Stability`` (optional) - Stability of the pMHC-I complex * - ``Half Life`` (optional) - Half-life of the pMHC-I complex * - ``Stability Rank`` (optional) - The % rank stability of the pMHC-I complex * - ``NetMHCstab allele`` (optional) - Nearest neighbor to the ``HLA Allele``. Used for NetMHCstab prediction * - ``Reference Match`` (T/F) (optional) - Was there a BLAST match of the mutated peptide sequence to the reference proteome? filtered.tsv.reference_matches Report Columns --------------------------------------------- This file is only generated when the ``--run-reference-proteome-similarity`` option is chosen. .. list-table:: :header-rows: 1 * - Column Name - Description * - ``Chromosome`` - The chromosome of this variant * - ``Start`` - The start position of this variant in the zero-based, half-open coordinate system * - ``Stop`` - The stop position of this variant in the zero-based, half-open coordinate system * - ``Reference`` - The reference allele * - ``Variant`` - The alt allele * - ``Transcript`` - The Ensembl ID of the affected transcript * - ``Peptide`` - The peptide sequence submitted to BLAST * - ``Hit ID`` - The BLAST alignment hit ID (reference proteome sequence ID) * - ``Hit Definition`` - The BLAST alignment hit definition (reference proteome sequence name) * - ``Query Sequence`` - The BLAST query sequence * - ``Match Sequence`` - The BLAST match sequence * - ``Match Start`` - The match start position in the matched reference proteome sequence * - ``Match Stop`` - The match stop position in the matched reference proteome sequence