diff --git a/CRISPResso2/CRISPRessoPooledCORE.py b/CRISPResso2/CRISPRessoPooledCORE.py
index 6cdeea0c..acd101db 100644
--- a/CRISPResso2/CRISPRessoPooledCORE.py
+++ b/CRISPResso2/CRISPRessoPooledCORE.py
@@ -161,9 +161,17 @@ def calculate_aligned_samtools_exclude_flags(samtools_exclude_flags):
     by filtering 0x900 (not primary alignment and supplementary alignment)
     and also including any other user specified filters.
     """
-    samtools_exclude_flags = int(samtools_exclude_flags, base=16)
+    if ',' in samtools_exclude_flags:
+        return f'{samtools_exclude_flags},{hex(0x900)}'
+    elif samtools_exclude_flags.startswith('0x'):
+        samtools_exclude_flags = int(samtools_exclude_flags, base=16)
+    elif samtools_exclude_flags.startswith('0'):
+        samtools_exclude_flags = int(samtools_exclude_flags, base=8)
+    else:
+        samtools_exclude_flags = int(samtools_exclude_flags)
     return hex(0x900 | samtools_exclude_flags)
 
+
 def get_n_aligned_bam(bam_filename, samtools_exclude_flags):
     p = sb.Popen(f"samtools view -F {calculate_aligned_samtools_exclude_flags(samtools_exclude_flags)} -c {bam_filename}", shell=True, stdout=sb.PIPE)
     return int(p.communicate()[0])
diff --git a/tests/unit_tests/test_CRISPRessoPooledCORE.py b/tests/unit_tests/test_CRISPRessoPooledCORE.py
index c7bc36af..86a02bc1 100644
--- a/tests/unit_tests/test_CRISPRessoPooledCORE.py
+++ b/tests/unit_tests/test_CRISPRessoPooledCORE.py
@@ -15,3 +15,13 @@ def test_calculate_aligned_samtools_exclude_flags_9():
 
 def test_calculate_aligned_samtools_exclude_flags_0x100():
     assert CRISPRessoPooledCORE.calculate_aligned_samtools_exclude_flags('0x100') == hex(0x900)
+
+
+def test_calculate_aligned_samtools_exclude_flags_010():
+    """This tests for proper handling of octal numbers."""
+    assert CRISPRessoPooledCORE.calculate_aligned_samtools_exclude_flags('010') == hex(0x908)
+
+
+def test_calculate_aligned_samtools_exclude_flags_comma():
+    """This tests for proper handling of commas."""
+    assert CRISPRessoPooledCORE.calculate_aligned_samtools_exclude_flags('0,4') == f'0,4,{hex(0x900)}'