removing duplicate calls from pindel

snakecnv/bin/parse.py

@@ -42,6 +42,9 @@ def convert_svtool_to_vcf(reference, inputfile, gaps, outputfile,
     # Merging records (necessary for delly inversions)
     records = SVReader.bnd_merge(svtype, records)
 
+    # Removing duplicated entries (only performed for pindel records)
+    records = SVReader.remove_duplicate(records)
+
     # Now filtering the records
     if not doNotFilter:
         eprint("Now filtering")