Merge branch 'hotfix/1.5.5'

cancerit · May 9, 2016 · ec28e2c · ec28e2c
2 parents cb80d0a + aa431b1
commit ec28e2c
Showing 1 changed file with 28 additions and 2 deletions.
diff --git a/config/human/flag.vcf.config.ini b/config/human/flag.vcf.config.ini
@@ -118,13 +118,39 @@ minPassPhaseQual=21
 minDepthQual=25
 minNormMutAllelequal=15
 minRdPosDepth=8
+vcfUnmatchedMinMutAlleleCvg=3
+vcfUnmatchedMinSamplePct=1
+matchedNormalMaxMutProportion=0.2
+minSingleEndCoverage=10
 
 [HUMAN_AMPLICON FLAGLIST]
 flagList=<<LST
+depthFlag
+readPositionFlag
+matchedNormalFlag
+pentamericMotifFlag
+avgMapQualFlag
+simpleRepeatFlag
+centromericRepeatFlag
+codingFlag
+snpFlag
+phasingFlag
+tumIndelDepthFlag
+hiSeqDepthFlag
+annotationFlag
+unmatchedNormalVcfFlag
+singleEndFlag
+matchedNormalProportion
 LST
 
-[HUMAN_AMPLICON BEDFILES]
-
+[HUMAN_FOLLOWUP BEDFILES]
+centromericRepeatBed=centromeric_repeats.bed
+simpleRepeatBed=simple_repeats.bed
+snpBed=snps.bed
+annotatableBed=Human.GRCh37.gene_regions.bed.gz
+codingBed=Human.GRCh37.codingexon_regions.sub.bed.gz
+germlineIndelBed=
+highSeqDepthBed=hi_seq_depth.bed
 
 [HUMAN_RNASEQ FLAGLIST]
 flagList=<<LST