fix: remove exomdepth output =1

clinical-genomics-uppsala · Aug 21, 2023 · 8556e33 · 8556e33
1 parent db1197e
commit 8556e33
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/workflow/scripts/exomedepth_export.R b/workflow/scripts/exomedepth_export.R
@@ -7,7 +7,10 @@ cnv_call_df <- data.frame(
   )
 
 if (length(all.exons@CNV.calls) > 0) {
-
+
+  # for compatability with alissa remove rows where there is no-change (reads.ratio == 1)
+  cnv_call_df <- cnv_call_df[cnv_call_df$reads.ratio != 1, ] 
+
   # Create Nexus SV format text file
   nexus <- c("id", "reads.ratio")
   nexus_df <- cnv_call_df[nexus]