4.0.1.0
Tool documentation for GATK release 4.0.1.0
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* Tool Documentation Index
Copy Number Variant Discovery Tools that analyze read coverage to detec... -
AccumulateVariantCallingMetrics (Picard)
Combines multiple Variant Calling Metrics files into a single file. Th... -
AddCommentsToBam (Picard)
Adds comments to the header of a BAM file.This tool makes a copy of the... -
AddOATag (Picard)
This tool takes in an aligned SAM or BAM and adds the OA tag to every a... -
AddOrReplaceReadGroups (Picard)
Assigns all the reads in a file to a single new read-group. This tool ... -
AlignmentAgreesWithHeaderReadFilter
Filters out reads where the alignment does not match the contents of th... -
AlleleFraction
Variant allele fraction for a genotype Category Variant Annota... -
AllowAllReadsReadFilter
Do not filter out any read Category Read Filters Over... -
AmbiguousBaseReadFilter
Filters out reads that have greater than the threshold number of N base... -
AnalyzeCovariates
Evaluate and compare base quality score recalibration (BQSR) tables ... -
AnalyzeSaturationMutagenesis (BETA)
(EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutag... -
AnnotateIntervals (BETA)
Annotates intervals with GC content Category Copy Number Varia... -
AnnotatePairOrientation (BETA)
(EXPERIMENTAL) Annotate a non-M2 VCF (using the associated tumor bam) w... -
AnnotateVcfWithBamDepth
(Internal) Annotate a vcf with a bam's read depth at each variant locus... -
AnnotateVcfWithExpectedAlleleFraction
(Internal) Annotate a vcf with expected allele fractions in pooled sequ... -
ApplyBQSR
Apply base quality score recalibration Category Read Data Mani... -
ApplyBQSRSpark (BETA)
Apply base quality score recalibration on Spark Category Read ... -
ApplyVQSR
Apply a score cutoff to filter variants based on a recalibration table... -
ASEReadCounter
Generates table of filtered base counts at het sites for allele specifi... -
AS_BaseQualityRankSumTest
Allele-specific rank sum test of REF versus ALT base quality scores (AS... -
AS_FisherStrand
Allele-specific strand bias estimated using Fisher's exact test (AS_FS)... -
AS_InbreedingCoeff
Allele-specific likelihood-based test for the consanguinity among sampl... -
AS_MappingQualityRankSumTest
Allele-specific rank sum test for mapping qualities of REF versus ALT r... -
AS_QualByDepth
Allele-specific call confidence normalized by depth of sample reads sup... -
AS_ReadPosRankSumTest
Allele-specific rank sum test for relative positioning of REF versus AL... -
AS_RMSMappingQuality
Allele-specific root-mean-square of the mapping quality of reads across... -
AS_StrandOddsRatio
Allele-specific strand bias estimated by the symmetric odds ratio test ... -
BaitDesigner (Picard)
Designs oligonucleotide baits for hybrid selection reactions.This tool ... -
BamIndexStats (Picard)
Generate index statistics from a BAM fileThis tool calculates statistic... -
BamToBfq (Picard)
Converts a BAM file into a BFQ (binary fastq formatted) file.The BFQ fo...