Mercurial > repos > iuc > gatk2

diff gatk2_annotations.txt.sample @ 6:b80301676614 draft

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Uploaded
author iuc
date Wed, 18 Feb 2015 11:36:59 -0500
parents c2645201ffae
children
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--- a/gatk2_annotations.txt.sample	Tue Mar 11 07:42:09 2014 -0400
+++ b/gatk2_annotations.txt.sample	Wed Feb 18 11:36:59 2015 -0500
@@ -1,6 +1,5 @@
 #unique_id	name	gatk_value	tools_valid_for
-#http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk
-AlleleBalance	AlleleBalance	AB	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
+AlleleBalance	AlleleBalance	AlleleBalance	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
@@ -13,7 +12,6 @@
 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,HaplotypeCaller
 MVLikelihoodRatio	MVLikelihoodRatio	MVLikelihoodRatio	VariantAnnotator,VariantRecalibrator,HaplotypeCaller
 MappingQualityRankSumTest	MappingQualityRankSumTest	MappingQualityRankSumTest	UnifiedGenotyper,VariantAnnotator,VariantRecalibrator,HaplotypeCaller
@@ -26,20 +24,3 @@
 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
-