Filtering Commands

pVAC-Seq currently offers two filters: a binding filter and a coverage filter.

The binding filter is always run automatically as part of the pVAC-Seq pipeline. The coverage filter is run automatically if bam-readcount or cufflinks file are provided as additional input files to a pVAC-Seq run.

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

Binding Filter

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. 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 pVAC-Seq 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.

The binding filter also offers the option to filter on Fold Change columns, which contain the ratio of the MT score to the WT Score. If the binding filter is set to “best”, the “Corresponding Fold Change” column will be used. (“Corresponding WT Score”/”Best MT Score”). If the binding filter is set to “median”, the “Median Fold Change” column will be used (“Median WT Score”/”Median MT Score”).

usage: pvacseq binding_filter [-h] [-b BINDING_THRESHOLD]
                              [-c MINIMUM_FOLD_CHANGE] [-m {lowest,median}]
                              input_file output_file
Required 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
-b=500, --binding-threshold=500
 Report only epitopes where the mutant allele has ic50 binding scores below this value. Default: 500
-c=0, --minimum-fold-change=0
 Minimum fold change between mutant binding score and wild-type score. The default is 0, which filters no results, but 1 is often a sensible option (requiring that binding is better to the MT than WT). Default: 0
-m="median", --top-score-metric="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

Possible choices: lowest, median

Coverage Filter

If a pVAC-Seq process has been run with bam-readcount or Cufflinks input files then the coverage_filter can be run again on the final report file to narrow down the results even further.

If no additional coverage input files have been provided to the main pVAC-Seq run then this information would need to be manually added to the report in order to run this filter.

usage: pvacseq coverage_filter [-h] [--normal-cov NORMAL_COV]
                               [--tdna-cov TDNA_COV] [--trna-cov TRNA_COV]
                               [--normal-vaf NORMAL_VAF] [--tdna-vaf TDNA_VAF]
                               [--trna-vaf TRNA_VAF] [--expn-val EXPN_VAL]
                               input_file output_file
Required Arguments
input_file The final report .tsv file to filter
output_file Output .tsv file containing list of filtered epitopes based on coverage and expression values
Optional Arguments
--normal-cov=5 Normal Coverage Cutoff. Sites above this cutoff will be considered. Default: 5
--tdna-cov=10 Tumor DNA Coverage Cutoff. Sites above this cutoff will be considered. Default: 10
--trna-cov=10 Tumor RNA Coverage Cutoff. Sites above this cutoff will be considered. Default: 10
--normal-vaf=2 Normal VAF Cutoff. Sites BELOW this cutoff in normal will be considered. Default: 2
--tdna-vaf=40 Tumor DNA VAF Cutoff. Sites above this cutoff will be considered. Default: 40
--trna-vaf=40 Tumor RNA VAF Cutoff. Sites above this cutoff will be considered. Default: 40
--expn-val=1 Gene and Transcript Expression cutoff. Sites above this cutoff will be consideredDefault: 1