Merge branch 'hotfix/1.8.5'

cancerit · Sep 11, 2018 · fa48fed · fa48fed
2 parents 19e1c68 + e7b7c68
commit fa48fed
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Showing 4 changed files with 60 additions and 2 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 1.8.5
+
+* Added TARGETED to GRCh38 human config ini
+
 ## 1.8.4
 
 * added 3 soft flags (CLPM, ASMD and ASRD) to all species builds and design_types (except RNAseq)

diff --git a/config/Human/GRCh38/flag.vcf.config.ini b/config/Human/GRCh38/flag.vcf.config.ini
@@ -199,3 +199,57 @@ minPassPhaseQual=21
 minDepthQual=25
 minNormMutAllelequal=15
 minRdPosDepth=8
+
+[HUMAN_TARGETED PARAMS]
+keepSW=0
+minAnalysedQual=11
+maxMatchedNormalAlleleProportion=0.03
+maxPhasingMinorityStrandReadProportion=0.04
+readPosBeginningOfReadIgnoreProportion=0.08
+readPosTwoThirdsOfReadExtendProportion=0.08
+pentamerMinPassAvgQual=20
+samePosMaxPercent=80
+maxTumIndelProportion=10
+maxNormIndelProportion=10
+minPassAvgMapQual=21
+minPassPhaseQual=21
+minDepthQual=25
+minNormMutAllelequal=15
+minRdPosDepth=8
+vcfUnmatchedMinMutAlleleCvg=3
+vcfUnmatchedMinSamplePct=1
+matchedNormalMaxMutProportion=0.2
+minSingleEndCoverage=10
+
+[HUMAN_TARGETED FLAGLIST]
+flagList=<<LST
+depthFlag
+readPositionFlag
+matchedNormalFlag
+pentamericMotifFlag
+avgMapQualFlag
+simpleRepeatFlag
+centromericRepeatFlag
+codingFlag
+snpFlag
+phasingFlag
+tumIndelDepthFlag
+sameReadPosFlag
+hiSeqDepthFlag
+annotationFlag
+unmatchedNormalVcfFlag
+singleEndFlag
+matchedNormalProportion
+alignmentScoreReadLengthAdjustedFlag
+clippingMedianFlag
+alnScoreMedianFlag
+LST
+
+[HUMAN_TARGETED BEDFILES]
+centromericRepeatBed=centromeric_repeats.bed.gz
+simpleRepeatBed=simple_repeats.bed.gz
+snpBed=snps.bed.gz
+annotatableBed=gene_regions.bed.gz
+codingBed=codingexon_regions.sub.bed.gz
+germlineIndelBed=
+highSeqDepthBed=hi_seq_depth.bed.gz
diff --git a/lib/Sanger/CGP/CavemanPostProcessing.pm b/lib/Sanger/CGP/CavemanPostProcessing.pm
@@ -32,7 +32,7 @@ use Attribute::Abstract;
 use Data::Dumper;
 use base 'Exporter';
 
-our $VERSION = '1.8.2';
+our $VERSION = '1.8.5';
 our @EXPORT = qw($VERSION);
 
 const my $MATCH_CIG => 'M';

diff --git a/lib/Sanger/CGP/CavemanPostProcessor.pm b/lib/Sanger/CGP/CavemanPostProcessor.pm
@@ -32,7 +32,7 @@ use Attribute::Abstract;
 use Data::Dumper;
 use base 'Exporter';
 
-our $VERSION = '1.8.4';
+our $VERSION = '1.8.5';
 our @EXPORT = qw($VERSION);
 
 const my $MATCH_CIG => 'M';