4.6.0.0
Tool documentation for GATK release 4.6.0.0
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* Tool Documentation Index
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AccumulateQualityYieldMetrics (Picard)
Combines multiple QualityYieldMetrics files into a single file.... -
AccumulateVariantCallingMetrics (Picard)
Combines multiple Variant Calling Metrics files into a single f... -
AddCommentsToBam (Picard)
Adds comments to the header of a BAM file.This tool makes a cop... -
AddFlowSNVQuality (EXPERIMENTAL)
Add SNV Quality to the flow-based CRAM Category Flow B... -
AddOATag (Picard)
This tool takes in an aligned SAM or BAM and adds the OA tag to... -
AddOrReplaceReadGroups (Picard)
Assigns all the reads in a file to a single new read-group. Th... -
AlignmentAgreesWithHeaderReadFilter
Filters out reads where the alignment does not match the conten... -
AlignmentSummaryMetrics
Back to Tool Docs Index Alignment metrics Ca... -
AlleleFraction
Variant allele fraction for a genotype Category Varian... -
AlleleFrequencyQCMetric
Back to Tool Docs Index Metrics Category ... -
AllelePseudoDepth
Total depth of coverage per sample and over all samples (DP) ... -
AllowAllReadsReadFilter
Do not filter out any read Category Read Filters ... -
AmbiguousBaseReadFilter
Filters out reads that have greater than the threshold number o... -
AnalyzeCovariates
Evaluate and compare base quality score recalibration (BQSR) ta... -
AnalyzeSaturationMutagenesis (BETA)
(EXPERIMENTAL) Processes reads from a MITESeq or other saturati... -
AnnotateIntervals
Annotates intervals with GC content, mappability, and segmental... -
AnnotateVcfWithBamDepth
(Internal) Annotate a vcf with a bam's read depth at each varia... -
AnnotateVcfWithExpectedAlleleFraction
(Internal) Annotate a vcf with expected allele fractions in poo... -
ApplyBQSR
Apply base quality score recalibration Category Read D... -
ApplyBQSRSpark (BETA)
Apply base quality score recalibration on Spark Category ... -
ApplyVQSR
Apply a score cutoff to filter variants based on a recalibrati... -
ArraysControlCodesSummaryMetrics
Back to Tool Docs Index Metrics Category ... -
ArraysVariantCallingDetailMetrics
Back to Tool Docs Index Metrics Category ... -
ArraysVariantCallingSummaryMetrics
Back to Tool Docs Index Metrics Category ... -
ASEReadCounter
Generates table of filtered base counts at het sites for allele... -
AssemblyComplexity
Describe the complexity of an assembly region Category ... -
AS_BaseQualityRankSumTest
Allele-specific rank sum test of REF versus ALT base quality sc... -
AS_FisherStrand
Allele-specific strand bias estimated using Fisher's exact test... -
AS_InbreedingCoeff
Allele-specific likelihood-based test for the consanguinity amo...