Merge pull request #85 from vyepez88/code_cleaning

var freq in cohort added
gagneurlab · Jul 7, 2020 · 6322b36 · 6322b36
2 parents 0805ecf + 1ae9219
commit 6322b36
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/drop/configHelper.py b/drop/configHelper.py
@@ -154,8 +154,9 @@ def setDefaults(self, config, method=None):
             setKey(config, ["mae"], "gatkIgnoreHeaderCheck", True, verbose=VERBOSE)
             setKey(config, ["mae"], "padjCutoff", .05, verbose=VERBOSE)
             setKey(config, ["mae"], "allelicRatioCutoff", 0.8, verbose=VERBOSE)
+            setKey(config, ["mae"], "addAF", False, verbose=VERBOSE)
             setKey(config, ["mae"], "maxAF", .001, verbose=VERBOSE)
-            setKey(config, ["mae"], "gnomAD", False, verbose=VERBOSE)
+            setKey(config, ["mae"], "maxVarFreqCohort", .05, verbose=VERBOSE)
             setKey(config, ["mae"], "groups", None, verbose=VERBOSE)
             setKey(config, ["mae"], "qcGroups", None, verbose=VERBOSE)
 

diff --git a/drop/modules/mae-pipeline b/drop/modules/mae-pipeline
diff --git a/drop/template/config.yaml b/drop/template/config.yaml
@@ -59,6 +59,7 @@ mae:
     allelicRatioCutoff: 0.8
     addAF: false
     maxAF: .001
+    maxVarFreqCohort: .05
     # VCF-BAM matching
     qcVcf:        # path to common variant file e.g. qc_vcf_1000G.vcf.gz
     qcGroups: mae