Mercurial > repos > iuc > gatk2

diff gatk2_annotations.txt.sample @ 5:c2645201ffae draft

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Uploaded
author iuc
date Tue, 11 Mar 2014 07:42:09 -0400
parents 9ad15075b9fa
children b80301676614
line wrap: on
line diff
--- a/gatk2_annotations.txt.sample	Sat Jan 18 07:00:26 2014 -0500
+++ b/gatk2_annotations.txt.sample	Tue Mar 11 07:42:09 2014 -0400
@@ -1,30 +1,45 @@
 #unique_id	name	gatk_value	tools_valid_for
-AlleleBalance	AlleleBalance	AlleleBalance	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-AlleleBalanceBySample	AlleleBalanceBySample	AlleleBalanceBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-BaseCounts	BaseCounts	BaseCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-BaseQualityRankSumTest	BaseQualityRankSumTest	BaseQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-ChromosomeCounts	ChromosomeCounts	ChromosomeCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-DepthOfCoverage	DepthOfCoverage	DepthOfCoverage	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-DepthPerAlleleBySample	DepthPerAlleleBySample	DepthPerAlleleBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-FisherStrand	FisherStrand	FisherStrand	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-GCContent	GCContent	GCContent	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-HaplotypeScore	HaplotypeScore	HaplotypeScore	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-HardyWeinberg	HardyWeinberg	HardyWeinberg	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-HomopolymerRun	HomopolymerRun	HomopolymerRun	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-InbreedingCoeff	InbreedingCoeff	InbreedingCoeff	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+#http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk
+AlleleBalance	AlleleBalance	AB	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+AlleleBalanceBySample	AlleleBalanceBySample	AlleleBalanceBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+BaseCounts	BaseCounts	BaseCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+BaseQualityRankSumTest	BaseQualityRankSumTest	BaseQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+ChromosomeCounts	ChromosomeCounts	ChromosomeCounts	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+Coverage	Coverage	Coverage	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+DepthPerAlleleBySample	DepthPerAlleleBySample	DepthPerAlleleBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+FisherStrand	FisherStrand	FisherStrand	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+GCContent	GCContent	GCContent	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+HaplotypeScore	HaplotypeScore	HaplotypeScore	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+HardyWeinberg	HardyWeinberg	HardyWeinberg	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+HomopolymerRun	HomopolymerRun	HomopolymerRun	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+InbreedingCoeff	InbreedingCoeff	InbreedingCoeff	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
 IndelType	IndelType	IndelType	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-LowMQ	LowMQ	LowMQ	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MVLikelihoodRatio	MVLikelihoodRatio	MVLikelihoodRatio	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MappingQualityRankSumTest	MappingQualityRankSumTest	MappingQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MappingQualityZero	MappingQualityZero	MappingQualityZero	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MappingQualityZeroBySample	MappingQualityZeroBySample	MappingQualityZeroBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-MappingQualityZeroFraction	MappingQualityZeroFraction	MappingQualityZeroFraction	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-NBaseCount	NBaseCount	NBaseCount	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-QualByDepth	QualByDepth	QualByDepth	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-RMSMappingQuality	RMSMappingQuality	RMSMappingQuality	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-ReadDepthAndAllelicFractionBySample	ReadDepthAndAllelicFractionBySample	ReadDepthAndAllelicFractionBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-ReadPosRankSumTest	ReadPosRankSumTest	ReadPosRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-SampleList	SampleList	SampleList	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-SnpEff	SnpEff	SnpEff	VariantAnnotator,VariantRecalibrator
-SpanningDeletions	SpanningDeletions	SpanningDeletions	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
-TechnologyComposition	TechnologyComposition	TechnologyComposition	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+LowMQ	LowMQ	LowMQ	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+MVLikelihoodRatio	MVLikelihoodRatio	MVLikelihoodRatio	VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+MappingQualityRankSumTest	MappingQualityRankSumTest	MappingQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+MappingQualityZero	MappingQualityZero	MappingQualityZero	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+MappingQualityZeroBySample	MappingQualityZeroBySample	MappingQualityZeroBySample	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+NBaseCount	NBaseCount	NBaseCount	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+QualByDepth	QualByDepth	QualByDepth	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+RMSMappingQuality	RMSMappingQuality	RMSMappingQuality	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+ReadPosRankSumTest	ReadPosRankSumTest	ReadPosRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+SampleList	SampleList	SampleList	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+SnpEff	SnpEff	SnpEff	VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+SpanningDeletions	SpanningDeletions	SpanningDeletions	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+VariantType	VariantType	VariantType	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+AlleleCount	Allele count in genotypes, for each ALT allele (AC)	AC	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+AlleleFrequency	Allele Frequency, for each ALT allele (AF)	AF	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+AlleleNumber	Total number of alleles in called genotypes (AN)	AN	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+Coverage	Unfiltered depth over all samples (DP)	DP	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+Dels	Dels	Dels	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MQ	RMS Mapping Quality	MQ	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+MQ0	Mapping Quality Zero	MQ0	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+BaseQualityRankSumTest	BaseQualityRankSumTest	BaseQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+MappingQualityRankSumTest	MappingQualityRankSumTest	MappingQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+ReadPosRankSumTest	ReadPosRankSumTest	ReadPosRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+HaplotypeScore	HaplotypeScore	HaplotypeScore	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+QualByDepth	QualByDepth	QD	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+VQSLOD	Variant quality score recalibration	VQSLOD	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+FisherStrand	FisherStrand	FS	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+StrandBias	Strand Bias evidence (higher SB, more bias, more false positive calls)	SB	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+