pVACfuse logo

Filtering Commands

pVACfuse currently offers two filters: a binding filter and a top score filter.

The binding filter and top score filter are always run automatically as part of the pVACfuse pipeline.

All filters can also be run manually to narrow the final results down further.

Binding Filter

Using TensorFlow backend.
/home/docs/checkouts/readthedocs.org/user_builds/pvactools/conda/latest/lib/python3.5/site-packages/requests/__init__.py:91: RequestsDependencyWarning: urllib3 (1.24.1) or chardet (3.0.4) doesn't match a supported version!
  RequestsDependencyWarning)
usage: pvacfuse binding_filter [-h] [-b BINDING_THRESHOLD]
                               [-m {lowest,median}] [--exclude-NAs] [-a]
                               input_file output_file

positional arguments:
  input_file            The final report .tsv file to filter
  output_file           Output .tsv file containing list of filtered epitopes
                        based on binding affinity

optional arguments:
  -h, --help            show this help message and exit
  -b BINDING_THRESHOLD, --binding-threshold BINDING_THRESHOLD
                        Report only epitopes where the mutant allele has ic50
                        binding scores below this value. Default: 500
  -m {lowest,median}, --top-score-metric {lowest,median}
                        The ic50 scoring metric to use when filtering epitopes
                        by binding-threshold or minimum fold change. lowest:
                        Best MT Score/Corresponding Fold Change - lowest MT
                        ic50 binding score/corresponding fold change of all
                        chosen prediction methods. median: Median MT
                        Score/Median Fold Change - median MT ic50 binding
                        score/fold change of all chosen prediction methods.
                        Default: median
  --exclude-NAs         Exclude NA values from the filtered output. Default:
                        False
  -a, --allele-specific-binding-thresholds
                        Use allele-specific binding thresholds. To print the
                        allele-specific binding thresholds run `pvacfuse
                        allele_specific_cutoffs`. If an allele does not have a
                        special threshold value, the `--binding-threshold`
                        value will be used. Default: False

The binding filter filters out variants that don’t pass the chosen binding threshold. The user can chose whether to apply this filter to the lowest or the median binding affinity score by setting the --top-score-metric flag. The lowest binding affinity score is recorded in the Best MT Score column and represents the lowest ic50 score of all prediction algorithms that were picked during the previous pVACseq run. The median binding affinity score is recorded in the Median MT Score column and corresponds to the median ic50 score of all prediction algorithms used to create the report. Be default, the binding filter runs on the median binding affinity.

By default, entries with NA values will be included in the output. This behavior can be turned off by using the --exclude-NAs flag.

Top Score Filter

Using TensorFlow backend.
/home/docs/checkouts/readthedocs.org/user_builds/pvactools/conda/latest/lib/python3.5/site-packages/requests/__init__.py:91: RequestsDependencyWarning: urllib3 (1.24.1) or chardet (3.0.4) doesn't match a supported version!
  RequestsDependencyWarning)
usage: pvacfuse top_score_filter [-h] [-m {lowest,median}]
                                 input_file output_file

positional arguments:
  input_file            The final report .tsv file to filter
  output_file           Output .tsv file containing only the list of the top
                        epitope per variant

optional arguments:
  -h, --help            show this help message and exit
  -m {lowest,median}, --top-score-metric {lowest,median}
                        The ic50 scoring metric to use for filtering. lowest:
                        Best MT Score - lowest MT ic50 binding score of all
                        chosen prediction methods. median: Median MT Score -
                        median MT ic50 binding score of all chosen prediction
                        methods. Default: median

This filter picks the top epitope for a variant. By default the --top-score-metric option is set to median which will apply this filter to the Median MT Score column and pick the epitope with the lowest median mutant ic50 score for each variant. If the --top-score-metric option is set to lowest, the Best MT Score column is instead used to make this determination.