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

For usage instructions run

pvacseq binding_filter --help

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”).

Coverage Filter

For usage instructions run

pvacseq coverage_filter --help

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.