tumor-only germline prioritization: filter based on INFO/EPR

For tumor-only germline prioritization based on external databases, the
current approach wasn't doing much without `tumoronly_germline_filter` on,
resulting in confusing MultiQC reports with germline and somatic looking
identical. This uses the INFO/EPR column, instead of relying on the filter,
to restore the previous behavior with `LowPriority` filtering enabled.

HISTORY.md

@@ -1,3 +1,8 @@
+## 1.1.4 (in progress)
+
+- tumor-only germline prioritization: provide more useful germline filtering
+  based on prioritization INFO tag (EPR) rather than filter field.
+
 ## 1.1.3 (29 January 2019)
 
 - CNV: support background inputs for CNVkit, GATK4 CNV and seq2c. Allows

bcbio/variation/germline.py

@@ -221,6 +221,9 @@ def _is_somatic(rec):
     if status_flag is not None:
         if str(status_flag).lower() in ["somatic", "likelysomatic", "strongsomatic", "samplespecific"]:
             return True
+    epr = rec.INFO.get("EPR", "").split(",")
+    if epr and all([p == "pass" for p in epr]):
+        return True
     return False
 
 def _has_somatic_flag(rec):

setup.py

@@ -4,7 +4,7 @@
 import os
 from setuptools import setup, find_packages
 
-version = "1.1.3"
+version = "1.1.4a"
 
 def write_version_py():
     version_py = os.path.join(os.path.dirname(__file__), 'bcbio', 'pipeline',