Restore VAF>=5% cutoff for non-hotspots, from 4%

mskcc · Jun 29, 2018 · 1852bb3 · 1852bb3
1 parent cd44b75
commit 1852bb3
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/filter_dmp.R b/filter_dmp.R
@@ -18,7 +18,7 @@ annotate_maf <- function(maf) {
 
     if (!('FILTER' %in% names(maf))) maf$FILTER = '.'
     maf.annotated <- maf[, dmp_filter := ifelse(hotspot_whitelist == TRUE & as.numeric(t_depth) >= 12 & as.numeric(n_depth) >= 6 & as.numeric(t_alt_count) >= 3 & as.numeric(t_alt_count)/as.numeric(t_depth) >= 0.02, FALSE,
-                        ifelse(hotspot_whitelist == FALSE & as.numeric(t_depth) >= 20 & as.numeric(n_depth) >= 10 & as.numeric(t_alt_count) >= 5 & as.numeric(t_alt_count)/as.numeric(t_depth) >= 0.04, FALSE, TRUE))]
+                        ifelse(hotspot_whitelist == FALSE & as.numeric(t_depth) >= 20 & as.numeric(n_depth) >= 10 & as.numeric(t_alt_count) >= 5 & as.numeric(t_alt_count)/as.numeric(t_depth) >= 0.05, FALSE, TRUE))]
     maf.annotated <- maf[, FILTER := ifelse(dmp_filter == TRUE, ifelse((FILTER == '' | FILTER == '.' | FILTER == 'PASS'), 'dmp_filter', paste0(FILTER, ';dmp_filter')), FILTER)]
     return(maf.annotated)
 }