Allow indels that partially overlap repeat regions

ckandoth · ckandoth · commit ad6d3eefe3e3 · 2018-08-02T22:11:53.000-04:00
diff --git a/filter_blacklist_regions.R b/filter_blacklist_regions.R
@@ -13,12 +13,12 @@ annotate_maf <- function(maf, blacklist, rmsk) {
 
     blacklist_overlap <- foverlaps(maf[, .(Chromosome, Start_Position, End_Position)],
                                    blacklist,
-                                   type = "any",
+                                   type = "within",
                                    mult = "first")
 
     rmsk_overlap <- foverlaps(maf[, .(Chromosome, Start_Position, End_Position)],
                               rmsk,
-                              type = "any",
+                              type = "within",
                               mult = "first")
 
     if (!('FILTER' %in% names(maf))) maf$FILTER = '.'
