4.1.4.1
Tool documentation for GATK release 4.1.4.1
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* Tool Documentation Index
Copy Number Variant Discovery Tools that analyze read coverage to d... -
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... -
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... -
AlleleFraction
Variant allele fraction for a genotype Category Varian... -
AlleleFrequency
Stratify by eval RODs by the allele frequency of the alternate... -
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... -
AnnotatePairOrientation (EXPERIMENTAL)
Annotate a non-M2 VCF (using the associated tumor bam) with pai... -
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... -
ASEReadCounter
Generates table of filtered base counts at het sites for allele... -
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... -
AS_MappingQualityRankSumTest
Collects fragment counts at specified intervals Category Cover... -
AS_MappingQualityRankSumTest
Allele-specific rank sum test for mapping qualities of REF vers... -
AS_QualByDepth
Allele-specific call confidence normalized by depth of sample r... -
AS_ReadPosRankSumTest
Allele-specific rank sum test for relative positioning of REF v... -
AS_RMSMappingQuality
Allele-specific root-mean-square of the mapping quality of read... -
AS_StrandOddsRatio
Allele-specific strand bias estimated by the symmetric odds rat... -
BaitDesigner (Picard)
Designs oligonucleotide baits for hybrid selection reactions.Th...