diff --git a/mergesvvcf/mergedfile.py b/mergesvvcf/mergedfile.py
index 151b72a..c1975ba 100644
--- a/mergesvvcf/mergedfile.py
+++ b/mergesvvcf/mergedfile.py
@@ -197,9 +197,12 @@ def passed_variant(record):
             formats = []
             for hformat in vcf_reader.header.formats.itervalues():
                 num = None
-                if hformat.name == "GT" or hformat.number == "G":
-                    num = "G"
-                    continue  # Genotype is special cant do multiple
+                # if hformat.name == "GT" or hformat.number == "G":
+                #     num = "G"
+                #     continue  # Genotype is special cant do multiple
+                if hformat.name == "PL": num = "G"
+                if hformat.number == "G": num = "G"
+                if hformat.name == "GL": num = "3"
                 outvcf.header.formats.add(
                     "{}_{}".format(program, hformat.name),
                     num or hformat.number,
diff --git a/mergesvvcf/vcftobreakpoints.pyx b/mergesvvcf/vcftobreakpoints.pyx
index b1bafef..ab58ead 100644
--- a/mergesvvcf/vcftobreakpoints.pyx
+++ b/mergesvvcf/vcftobreakpoints.pyx
@@ -155,8 +155,10 @@ def breakpointsFromRecord(record):
         # defaults
         if chr2 is None:
             chr2 = chr1
-        if pos2 is None and "<" in altstr:
+        if pos2 is None and "<" in altstr and ">" in altstr:
             pos2 = record.stop
+        elif pos2 is None and re.match(r'^[ATCG]+$', altstr.strip(".")):
+            pos2 = record.pos + len(altstr.strip("."))
 
         # look for symbolic SVTYPE information in the alt field (eg, <DEL>)
         resultSym = re.match(__symbolicRE__, altstr)
@@ -189,7 +191,7 @@ def breakpointsFromRecord(record):
 
             reflen = len(ref)
             if pos2 is None:
-                pos2 = pos1 + reflen
+                pos2 = pos1 + len(altstr.strip("."))
             if svlen is None:
                 svlen = len(altstr) - reflen
             if svtype is None: