diff --git a/.idea/.name b/.idea/.name
new file mode 100644
index 000000000..7014f65a5
--- /dev/null
+++ b/.idea/.name
@@ -0,0 +1 @@
+cmi-gatk
\ No newline at end of file
diff --git a/.idea/ant.xml b/.idea/ant.xml
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+++ b/.idea/ant.xml
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diff --git a/.idea/codeStyleSettings.xml b/.idea/codeStyleSettings.xml
new file mode 100644
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+++ b/.idea/codeStyleSettings.xml
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diff --git a/.idea/compiler.xml b/.idea/compiler.xml
new file mode 100644
index 000000000..ded2e9a1d
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diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml
new file mode 100644
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--- /dev/null
+++ b/.idea/copyright/profiles_settings.xml
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\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
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+++ b/.idea/encodings.xml
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diff --git a/.idea/highlighting.xml b/.idea/highlighting.xml
new file mode 100644
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+++ b/.idea/highlighting.xml
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diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
new file mode 100644
index 000000000..b8c243dbe
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+++ b/.idea/inspectionProfiles/Project_Default.xml
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\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
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index 000000000..3b312839b
--- /dev/null
+++ b/.idea/inspectionProfiles/profiles_settings.xml
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\ No newline at end of file
diff --git a/.idea/libraries/GATK_libraries.xml b/.idea/libraries/GATK_libraries.xml
new file mode 100644
index 000000000..970d0a3dc
--- /dev/null
+++ b/.idea/libraries/GATK_libraries.xml
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\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
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diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
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diff --git a/.idea/scopes/scope_settings.xml b/.idea/scopes/scope_settings.xml
new file mode 100644
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--- /dev/null
+++ b/.idea/scopes/scope_settings.xml
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\ No newline at end of file
diff --git a/.idea/uiDesigner.xml b/.idea/uiDesigner.xml
new file mode 100644
index 000000000..3b0002030
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+++ b/.idea/uiDesigner.xml
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diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 000000000..cbc984988
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+++ b/.idea/vcs.xml
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diff --git a/.idea/workspace.xml b/.idea/workspace.xml
new file mode 100644
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+++ b/.idea/workspace.xml
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+ localhost
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+ cmi-gatk
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+ GATK libraries
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diff --git a/cmi-gatk.iml b/cmi-gatk.iml
new file mode 100644
index 000000000..e63aff535
--- /dev/null
+++ b/cmi-gatk.iml
@@ -0,0 +1,23 @@
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