Merge pull request #97 from UMCUGenetics/develop

Release v2.5.1

Author: rernst

settings/CPCT.ini

@@ -154,9 +154,9 @@ FILTER_SCALA	QScripts/HardFilter.scala
 FILTER_MODE	BOTH
 FILTER_SNPTYPES	SNP,NO_VARIATION
 FILTER_INDELTYPES	INDEL,MIXED
-FILTER_SNPNAME	LowQualityDepth	MappingQuality	StrandBias	HaplotypeScoreHigh	MQRankSumLow	ReadPosRankSumLow
+FILTER_SNPNAME	SNP_LowQualityDepth	SNP_MappingQuality	SNP_StrandBias	SNP_HaplotypeScoreHigh	SNP_MQRankSumLow	SNP_ReadPosRankSumLow
 FILTER_SNPEXPR	QD < 2.0	MQ < 40.0	FS > 60.0	HaplotypeScore > 13.0	MQRankSum < -12.5	ReadPosRankSum < -8.0
-FILTER_INDELNAME	LowQualityDepth	StrandBias	ReadPosRankSumLow
+FILTER_INDELNAME	INDEL_LowQualityDepth	INDEL_StrandBias	INDEL_ReadPosRankSumLow
 FILTER_INDELEXPR	QD < 2.0	FS > 200.0	ReadPosRankSum < -20.0
 FILTER_CLUSTERSIZE	3
 FILTER_CLUSTERWINDOWSIZE	35

settings/UMCU_MIPS.ini

@@ -123,9 +123,9 @@ FILTER_SCALA	QScripts/HardFilter.scala
 FILTER_MODE	BOTH
 FILTER_SNPTYPES	SNP,NO_VARIATION
 FILTER_INDELTYPES	INDEL,MIXED
-FILTER_SNPNAME	LowQualityDepth	MappingQuality	StrandBias	HaplotypeScoreHigh	MQRankSumLow	ReadPosRankSumLow
+FILTER_SNPNAME	SNP_LowQualityDepth	SNP_MappingQuality	SNP_StrandBias	SNP_HaplotypeScoreHigh	SNP_MQRankSumLow	SNP_ReadPosRankSumLow
 FILTER_SNPEXPR	QD < 2.0	MQ < 40.0	FS > 60.0	HaplotypeScore > 13.0	MQRankSum < -12.5	ReadPosRankSum < -8.0
-FILTER_INDELNAME	LowQualityDepth	StrandBias	ReadPosRankSumLow
+FILTER_INDELNAME	INDEL_LowQualityDepth	INDEL_StrandBias	INDEL_ReadPosRankSumLow
 FILTER_INDELEXPR	QD < 2.0	FS > 200.0	ReadPosRankSum < -20.0
 FILTER_CLUSTERSIZE	3
 FILTER_CLUSTERWINDOWSIZE	35

settings/hartwig_kg.ini

@@ -192,9 +192,9 @@ FILTER_SCALA	QScripts/HardFilter.scala
 FILTER_MODE	BOTH
 FILTER_SNPTYPES	SNP,NO_VARIATION
 FILTER_INDELTYPES	INDEL,MIXED
-FILTER_SNPNAME	LowQualityDepth	MappingQuality	StrandBias	HaplotypeScoreHigh	MQRankSumLow	ReadPosRankSumLow	HardToValidate	LowCoverage	VeryLowQual	LowQual	SOR
+FILTER_SNPNAME	SNP_LowQualityDepth	SNP_MappingQuality	SNP_StrandBias	SNP_HaplotypeScoreHigh	SNP_MQRankSumLow	SNP_ReadPosRankSumLow	SNP_HardToValidate	SNP_LowCoverage	SNP_VeryLowQual	SNP_LowQual	SNP_SOR
 FILTER_SNPEXPR	QD < 2.0	MQ < 40.0	FS > 60.0	HaplotypeScore > 13.0	MQRankSum < -12.5	ReadPosRankSum < -8.0	MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)	DP < 5	QUAL < 30	QUAL >= 30.0 && QUAL < 50.0 	SOR > 4.0
-FILTER_INDELNAME	LowQualityDepth	StrandBias	ReadPosRankSumLow	HardToValidate	LowCoverage	VeryLowQual	LowQual	SOR
+FILTER_INDELNAME	INDEL_LowQualityDepth	INDEL_StrandBias	INDEL_ReadPosRankSumLow	INDEL_HardToValidate	INDEL_LowCoverage	INDEL_VeryLowQual	INDEL_LowQual	INDEL_SOR
 FILTER_INDELEXPR	QD < 2.0	FS > 200.0	ReadPosRankSum < -20.0	MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)	DP < 5	QUAL < 30.0	QUAL >= 30.0 && QUAL < 50.0	SOR > 10.0
 FILTER_CLUSTERSIZE	3
 FILTER_CLUSTERWINDOWSIZE	10