Fig. 4

User filtering of variants. Screenshot showing multi-clause filtering dialogue box. Users can construct complex multi-clause filters from over 70 variant attributes or choose from common preset filters. PathOS automatically applies one or more flags (when uploading samples) to each variant based on its annotations. These flags are available for user filtering as shown in the filter being applied in the screen shot. The flags are listed with typical filtering criteria in parenthesis: pass: Passed all filters. vaf: Low variant allele frequency (<8% Somatic, < 15% Germline). vrd: Low total read depth (<100 reads). vad: Low variant read depth (<20 reads). blk: Assay specific variant black list (user defined). oor: Out of assay specific region of interest (user defined). con: Inferred benign consequences (system defined). gmaf: High global minor allele frequency (>1%). pnl: Frequently occurring variant in assay (>35%). sin: Singleton variant in replicate samples (not in both samples)