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Tools that analyze read coverage to detect copy number variants.

Name Summary
AnnotateIntervals Annotates intervals with GC content, mappability, and segmental-duplication content
CallCopyRatioSegments Calls copy-ratio segments as amplified, deleted, or copy-number neutral
CreateReadCountPanelOfNormals Creates a panel of normals for read-count denoising
DenoiseReadCounts Denoises read counts to produce denoised copy ratios
DetermineGermlineContigPloidy Determines the baseline contig ploidy for germline samples given counts data
FilterIntervals Filters intervals based on annotations and/or count statistics
GermlineCNVCaller Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy
ModelSegments Models segmented copy ratios from denoised read counts and segmented minor-allele fractions from allelic counts
PlotDenoisedCopyRatios Creates plots of denoised copy ratios
PlotModeledSegments Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates
PostprocessGermlineCNVCalls Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios

Tools that count coverage, e.g. depth per allele

Name Summary
ASEReadCounter Generates table of filtered base counts at het sites for allele specific expression
AnalyzeSaturationMutagenesis **BETA** (EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutagenesis experiment.
CollectAllelicCounts Collects reference and alternate allele counts at specified sites
CollectReadCounts Collects read counts at specified intervals
CountBases Count bases in a SAM/BAM/CRAM file
CountBasesSpark Counts bases in the input SAM/BAM
CountReads Count reads in a SAM/BAM/CRAM file
CountReadsSpark Counts reads in the input SAM/BAM
GetPileupSummaries **BETA** Tabulates pileup metrics for inferring contamination
Pileup Prints read alignments in samtools pileup format
PileupSpark **BETA** Prints read alignments in samtools pileup format

Tools that collect sequencing quality related and comparative metrics

Name Summary
AccumulateVariantCallingMetrics (Picard) Combines multiple Variant Calling Metrics files into a single file
AnalyzeCovariates Evaluate and compare base quality score recalibration (BQSR) tables
BamIndexStats (Picard) Generate index statistics from a BAM file
CalcMetadataSpark **BETA** (Internal) Collects read metrics relevant to structural variant discovery
CalculateContamination Calculate the fraction of reads coming from cross-sample contamination
CalculateFingerprintMetrics (Picard) Calculate statistics on fingerprints, checking their viability
CalculateReadGroupChecksum (Picard) Creates a hash code based on the read groups (RG).
CheckFingerprint (Picard) Computes a fingerprint from the supplied input (SAM/BAM or VCF) file and compares it to the provided genotypes
CheckPileup Compare GATK's internal pileup to a reference Samtools mpileup
CheckTerminatorBlock (Picard) Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise
ClusterCrosscheckMetrics (Picard) Clusters the results of a CrosscheckFingerprints run by LOD score
CollectAlignmentSummaryMetrics (Picard) Produces a summary of alignment metrics from a SAM or BAM file.
CollectBaseDistributionByCycle (Picard) Chart the nucleotide distribution per cycle in a SAM or BAM file
CollectBaseDistributionByCycleSpark **BETA** Collects base distribution per cycle in SAM/BAM/CRAM file(s).
CollectGcBiasMetrics (Picard) Collect metrics regarding GC bias.
CollectHiSeqXPfFailMetrics (Picard) Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.
CollectHsMetrics (Picard) Collects hybrid-selection (HS) metrics for a SAM or BAM file.
CollectIndependentReplicateMetrics (Picard) **EXPERIMENTAL** Estimates the rate of independent replication of reads within a bam.
CollectInsertSizeMetrics (Picard) Collect metrics about the insert size distribution of a paired-end library.
CollectInsertSizeMetricsSpark **BETA** Collects insert size distribution information on alignment data
CollectJumpingLibraryMetrics (Picard) Collect jumping library metrics.
CollectMultipleMetrics (Picard) Collect multiple classes of metrics.
CollectMultipleMetricsSpark **BETA** Runs multiple metrics collection modules for a given alignment file
CollectOxoGMetrics (Picard) Collect metrics to assess oxidative artifacts.
CollectQualityYieldMetrics (Picard) Collect metrics about reads that pass quality thresholds and Illumina-specific filters.
CollectQualityYieldMetricsSpark **BETA** Collects quality yield metrics from SAM/BAM/CRAM file(s).
CollectRawWgsMetrics (Picard) Collect whole genome sequencing-related metrics.
CollectRnaSeqMetrics (Picard) Produces RNA alignment metrics for a SAM or BAM file.
CollectRrbsMetrics (Picard) Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.
CollectSamErrorMetrics (Picard) Program to collect error metrics on bases stratified in various ways.
CollectSequencingArtifactMetrics (Picard) Collect metrics to quantify single-base sequencing artifacts.
CollectTargetedPcrMetrics (Picard) Calculate PCR-related metrics from targeted sequencing data.
CollectVariantCallingMetrics (Picard) Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file
CollectWgsMetrics (Picard) Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
CollectWgsMetricsWithNonZeroCoverage (Picard) **EXPERIMENTAL** Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
CompareBaseQualities Compares the base qualities of two SAM/BAM/CRAM files
CompareDuplicatesSpark **BETA** Determine if two potentially identical BAMs have the same duplicate reads
CompareMetrics (Picard) Compare two metrics files.
CompareSAMs (Picard) Compare two input ".sam" or ".bam" files.
ConvertSequencingArtifactToOxoG (Picard) Extract OxoG metrics from generalized artifacts metrics.
CrosscheckFingerprints (Picard) Checks that all data in the input files appear to have come from the same individual
EstimateLibraryComplexity (Picard) Estimates the numbers of unique molecules in a sequencing library.
FlagStat Accumulate flag statistics given a BAM file
FlagStatSpark Spark tool to accumulate flag statistics
GetSampleName **BETA** Emit a single sample name
MeanQualityByCycle (Picard) Collect mean quality by cycle.
MeanQualityByCycleSpark **BETA** MeanQualityByCycle on Spark
QualityScoreDistribution (Picard) Chart the distribution of quality scores.
QualityScoreDistributionSpark **BETA** QualityScoreDistribution on Spark
ValidateSamFile (Picard) Validates a SAM or BAM file.
ViewSam (Picard) Prints a SAM or BAM file to the screen

Tools that process genomic intervals in various formats

Name Summary
BedToIntervalList (Picard) Converts a BED file to a Picard Interval List.
IntervalListToBed (Picard) Converts an Picard IntervalList file to a BED file.
IntervalListTools (Picard) A tool for performing various IntervalList manipulations
LiftOverIntervalList (Picard) Lifts over an interval list from one reference build to another.
PreprocessIntervals Prepares bins for coverage collection
SplitIntervals Split intervals into sub-interval files.

Tools that perform metagenomic analysis, e.g. microbial community composition and pathogen detection

Name Summary
PathSeqBuildKmers Builds set of host reference k-mers
PathSeqBuildReferenceTaxonomy Builds a taxonomy datafile of the microbe reference
PathSeqBwaSpark Step 2: Aligns reads to the microbe reference
PathSeqFilterSpark Step 1: Filters low quality, low complexity, duplicate, and host reads
PathSeqPipelineSpark Combined tool that performs all steps: read filtering, microbe reference alignment, and abundance scoring
PathSeqScoreSpark Step 3: Classifies pathogen-aligned reads and generates abundance scores

Miscellaneous tools, e.g. those that aid in data streaming

Name Summary
CreateHadoopBamSplittingIndex **BETA** Create a Hadoop BAM splitting index
FifoBuffer (Picard) Provides a large, FIFO buffer that can be used to buffer input and output streams between programs.
FixCallSetSampleOrdering **EXPERIMENTAL** fix sample names in a shuffled callset
GatherBQSRReports Gathers scattered BQSR recalibration reports into a single file
GatherTranches **BETA** Gathers scattered VQSLOD tranches into a single file
IndexFeatureFile Creates an index for a feature file, e.g. VCF or BED file.
ParallelCopyGCSDirectoryIntoHDFSSpark **BETA** Parallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark
ReblockGVCF **BETA** Condenses homRef blocks in a single-sample GVCF

Tools that manipulate read data in SAM, BAM or CRAM format

Name Summary
AddCommentsToBam (Picard) Adds comments to the header of a BAM file.
AddOATag (Picard) Record current alignment information to OA tag.
AddOrReplaceReadGroups (Picard) Assigns all the reads in a file to a single new read-group.
ApplyBQSR Apply base quality score recalibration
ApplyBQSRSpark **BETA** Apply base quality score recalibration on Spark
BQSRPipelineSpark **BETA** Both steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark
BamToBfq (Picard) Converts a BAM file into a BFQ (binary fastq formatted) file
BaseRecalibrator Generates recalibration table for Base Quality Score Recalibration (BQSR)
BaseRecalibratorSpark **BETA** Generate recalibration table for Base Quality Score Recalibration (BQSR) on Spark
BuildBamIndex (Picard) Generates a BAM index ".bai" file.
BwaAndMarkDuplicatesPipelineSpark **BETA** Takes name-sorted file and runs BWA and MarkDuplicates.
BwaSpark **BETA** Align reads to a given reference using BWA on Spark
CleanSam (Picard) Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
ClipReads Clip reads in a SAM/BAM/CRAM file
ConvertHeaderlessHadoopBamShardToBam **BETA** Convert a headerless BAM shard into a readable BAM
DownsampleSam (Picard) Downsample a SAM or BAM file.
ExtractOriginalAlignmentRecordsByNameSpark **BETA** Subsets reads by name
FastqToSam (Picard) Converts a FASTQ file to an unaligned BAM or SAM file
FilterSamReads (Picard) Subsets reads from a SAM or BAM file by applying one of several filters.
FixMateInformation (Picard) Verify mate-pair information between mates and fix if needed.
FixMisencodedBaseQualityReads Fix Illumina base quality scores in a SAM/BAM/CRAM file
GatherBamFiles (Picard) Concatenate efficiently BAM files that resulted from a scattered parallel analysis
LeftAlignIndels Left-aligns indels from reads in a SAM/BAM/CRAM file
MarkDuplicates (Picard) Identifies duplicate reads.
MarkDuplicatesSpark MarkDuplicates on Spark
MarkDuplicatesWithMateCigar (Picard) Identifies duplicate reads, accounting for mate CIGAR.
MergeBamAlignment (Picard) Merge alignment data from a SAM or BAM with data in an unmapped BAM file.
MergeSamFiles (Picard) Merges multiple SAM and/or BAM files into a single file.
PositionBasedDownsampleSam (Picard) Downsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.
PrintReads Print reads in the SAM/BAM/CRAM file
PrintReadsSpark PrintReads on Spark
ReorderSam (Picard) Reorders reads in a SAM or BAM file to match ordering in a second reference file.
ReplaceSamHeader (Picard) Replaces the SAMFileHeader in a SAM or BAM file.
RevertBaseQualityScores Revert Quality Scores in a SAM/BAM/CRAM file
RevertOriginalBaseQualitiesAndAddMateCigar (Picard) Reverts the original base qualities and adds the mate cigar tag to read-group BAMs
RevertSam (Picard) Reverts SAM or BAM files to a previous state.
RevertSamSpark **BETA** Reverts SAM or BAM files to a previous state.
SamFormatConverter (Picard) Convert a BAM file to a SAM file, or a SAM to a BAM
SamToFastq (Picard) Converts a SAM or BAM file to FASTQ.
SetNmAndUqTags (Picard) DEPRECATED: Use SetNmMdAndUqTags instead.
SetNmMdAndUqTags (Picard) Fixes the NM, MD, and UQ tags in a SAM file
SimpleMarkDuplicatesWithMateCigar (Picard) **EXPERIMENTAL** Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.
SortSam (Picard) Sorts a SAM or BAM file
SortSamSpark **BETA** SortSam on Spark (works on SAM/BAM/CRAM)
SplitNCigarReads Split Reads with N in Cigar
SplitReads Outputs reads from a SAM/BAM/CRAM by read group, sample and library name
SplitSamByLibrary (Picard) Splits a SAM or BAM file into individual files by library
SplitSamByNumberOfReads (Picard) Splits a SAM or BAM file to multiple BAMs.
UmiAwareMarkDuplicatesWithMateCigar (Picard) **EXPERIMENTAL** Identifies duplicate reads using information from read positions and UMIs.
UnmarkDuplicates Clears the 0x400 duplicate SAM flag

Tools that analyze and manipulate FASTA format references

Name Summary
BaitDesigner (Picard) Designs oligonucleotide baits for hybrid selection reactions.
BwaMemIndexImageCreator Create a BWA-MEM index image file for use with GATK BWA tools
CountBasesInReference Count the numbers of each base in a reference file
CreateSequenceDictionary (Picard) Creates a sequence dictionary for a reference sequence.
ExtractSequences (Picard) Subsets intervals from a reference sequence to a new FASTA file.
FastaAlternateReferenceMaker Create an alternative reference by combining a fasta with a vcf.
FastaReferenceMaker Create snippets of a fasta file
FindBadGenomicKmersSpark **BETA** Identifies sequences that occur at high frequency in a reference
NonNFastaSize (Picard) Counts the number of non-N bases in a fasta file.
NormalizeFasta (Picard) Normalizes lines of sequence in a FASTA file to be of the same length.
ScatterIntervalsByNs (Picard) Writes an interval list created by splitting a reference at Ns.

Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)

Name Summary
CombineGVCFs Merges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations
GenomicsDBImport Import VCFs to GenomicsDB
GenotypeGVCFs Perform joint genotyping on one or more samples pre-called with HaplotypeCaller
GnarlyGenotyper **BETA** Perform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller
HaplotypeCaller Call germline SNPs and indels via local re-assembly of haplotypes
HaplotypeCallerSpark **BETA** HaplotypeCaller on Spark
Mutect2 Call somatic SNVs and indels via local assembly of haplotypes
ReadsPipelineSpark **BETA** Runs BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller on unaligned or aligned reads to generate a VCF.

Tools that detect structural variants

Name Summary
CpxVariantReInterpreterSpark **BETA** (Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf
DiscoverVariantsFromContigAlignmentsSAMSpark **BETA** (Internal) Examines aligned contigs from local assemblies and calls structural variants
ExtractSVEvidenceSpark **BETA** (Internal) Extracts evidence of structural variations from reads
FindBreakpointEvidenceSpark **BETA** (Internal) Produces local assemblies of genomic regions that may harbor structural variants
StructuralVariationDiscoveryPipelineSpark **BETA** Runs the structural variation discovery workflow on a single sample
SvDiscoverFromLocalAssemblyContigAlignmentsSpark **BETA** (Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints

Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine

Name Summary
AnnotatePairOrientation **EXPERIMENTAL** Annotate a non-M2 VCF (using the associated tumor bam) with pair orientation fields (e.g. F1R2 ).
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 sequencing
CalculateGenotypePosteriors Calculate genotype posterior probabilities given family and/or known population genotypes
CalculateMixingFractions (Internal) Calculate proportions of different samples in a pooled bam
Concordance **BETA** Evaluate concordance of an input VCF against a validated truth VCF
CountFalsePositives **BETA** Count PASS variants
CountVariants Counts variant records in a VCF file, regardless of filter status.
CountVariantsSpark CountVariants on Spark
EvaluateInfoFieldConcordance **BETA** Evaluate concordance of info fields in an input VCF against a validated truth VCF
FilterFuncotations **EXPERIMENTAL** Filter variants based on clinically-significant Funcotations.
FindMendelianViolations (Picard) Finds mendelian violations of all types within a VCF
FuncotateSegments **BETA** Functional annotation for segment files. The output formats are not well-defined and subject to change.
Funcotator Functional Annotator
FuncotatorDataSourceDownloader Data source downloader for Funcotator.
GenotypeConcordance (Picard) Calculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.
ValidateBasicSomaticShortMutations **EXPERIMENTAL** Check variants against tumor-normal bams representing the same samples, though not the ones from the actual calls.
ValidateVariants Validate VCF
VariantEval **BETA** General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
VariantsToTable Extract fields from a VCF file to a tab-delimited table

Tools that filter variants by annotating the FILTER column

Name Summary
ApplyVQSR Apply a score cutoff to filter variants based on a recalibration table
CNNScoreVariants Apply a Convolutional Neural Net to filter annotated variants
CNNVariantTrain **EXPERIMENTAL** Train a CNN model for filtering variants
CNNVariantWriteTensors **EXPERIMENTAL** Write variant tensors for training a CNN to filter variants
CreateSomaticPanelOfNormals **BETA** Make a panel of normals for use with Mutect2
FilterAlignmentArtifacts **EXPERIMENTAL** Filter alignment artifacts from a vcf callset.
FilterByOrientationBias **EXPERIMENTAL** Filter Mutect2 somatic variant calls using orientation bias
FilterMutectCalls Filter somatic SNVs and indels called by Mutect2
FilterVariantTranches Apply tranche filtering
FilterVcf (Picard) Hard filters a VCF.
VariantFiltration Filter variant calls based on INFO and/or FORMAT annotations
VariantRecalibrator Build a recalibration model to score variant quality for filtering purposes

Tools that manipulate variant call format (VCF) data

Name Summary
FixVcfHeader (Picard) Replaces or fixes a VCF header.
GatherVcfs (Picard) Gathers multiple VCF files from a scatter operation into a single VCF file
GatherVcfsCloud **BETA** Gathers multiple VCF files from a scatter operation into a single VCF file
LeftAlignAndTrimVariants Left align and trim vairants
LiftoverVcf (Picard) Lifts over a VCF file from one reference build to another.
MakeSitesOnlyVcf (Picard) Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
MergeVcfs (Picard) Combines multiple variant files into a single variant file
PrintVariantsSpark Prints out variants from the input VCF.
RemoveNearbyIndels (Internal) Remove indels from the VCF file that are close to each other.
RenameSampleInVcf (Picard) Renames a sample within a VCF or BCF.
SelectVariants Select a subset of variants from a VCF file
SortVcf (Picard) Sorts one or more VCF files.
SplitVcfs (Picard) Splits SNPs and INDELs into separate files.
UpdateVCFSequenceDictionary Updates the sequence dictionary in a variant file.
UpdateVcfSequenceDictionary (Picard) Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.
VariantAnnotator **BETA** Tool for adding annotations to VCF files
VcfFormatConverter (Picard) Converts VCF to BCF or BCF to VCF.
VcfToIntervalList (Picard) Converts a VCF or BCF file to a Picard Interval List

Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters

Name Summary
CheckIlluminaDirectory (Picard) Asserts the validity for specified Illumina basecalling data.
CollectIlluminaBasecallingMetrics (Picard) Collects Illumina Basecalling metrics for a sequencing run.
CollectIlluminaLaneMetrics (Picard) Collects Illumina lane metrics for the given BaseCalling analysis directory.
ExtractIlluminaBarcodes (Picard) Tool determines the barcode for each read in an Illumina lane.
IlluminaBasecallsToFastq (Picard) Generate FASTQ file(s) from Illumina basecall read data.
IlluminaBasecallsToSam (Picard) Transforms raw Illumina sequencing data into an unmapped SAM or BAM file.
MarkIlluminaAdapters (Picard) Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.

Tools that manipulate data generated by Genotyping arrays

Name Summary
CreateVerifyIDIntensityContaminationMetricsFile (Picard) Program to generate a picard metrics file from the output of the VerifyIDIntensity tool.
GtcToVcf (Picard) Program to convert a GTC file to a VCF
VcfToAdpc (Picard) Program to convert an Arrays VCF to an ADPC file.

Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM

Name Summary
MethylationTypeCaller **EXPERIMENTAL** Identify methylated bases from bisulfite sequenced, methylation-aware BAMs

Name Summary
AlleleFrequency Stratify by eval RODs by the allele frequency of the alternate allele

Applied by engine to select reads for analysis

Name Summary
AlignmentAgreesWithHeaderReadFilter Filters out reads where the alignment does not match the contents of the header
AllowAllReadsReadFilter Do not filter out any read
AmbiguousBaseReadFilter Filters out reads that have greater than the threshold number of N bases
CigarContainsNoNOperator Filter out reads with CIGAR containing N operator
FirstOfPairReadFilter Keep only reads that are first of pair
FragmentLengthReadFilter Keep only read pairs with insert length less than or equal to the given value
GoodCigarReadFilter Keep only reads containing good CIGAR string
HasReadGroupReadFilter Filter out reads without Read Group
IntervalOverlapReadFilter Filters out reads that don't overlap the specified region. NOTE: This approach to extracting overlapping reads is very slow compared to using PrintReads and -L on an indexed bam file.
LibraryReadFilter Keep only reads from the specified library
MappedReadFilter Filter out unmapped reads
MappingQualityAvailableReadFilter Filter out reads without available mapping quality
MappingQualityNotZeroReadFilter Filter out reads with mapping quality equal to zero
MappingQualityReadFilter Keep only reads with mapping qualities within a specified range
MatchingBasesAndQualsReadFilter Filter out reads where the bases and qualities do not match
MateDifferentStrandReadFilter Keep only reads with mates mapped on the different strand
MateOnSameContigOrNoMappedMateReadFilter Keep only reads whose mate maps to the same contig or is unmapped
MateUnmappedAndUnmappedReadFilter Filters reads whose mate is unmapped as well as unmapped reads.
MetricsReadFilter Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments
NonChimericOriginalAlignmentReadFilter Filters reads whose original alignment was chimeric.
NonZeroFragmentLengthReadFilter Filter out reads with fragment length different from zero
NonZeroReferenceLengthAlignmentReadFilter Filter out reads that do not align to the reference
NotDuplicateReadFilter Filter out reads marked as duplicate
NotSecondaryAlignmentReadFilter Filter out reads representing secondary alignments
NotSupplementaryAlignmentReadFilter Filter out reads representing supplementary alignments
OverclippedReadFilter Filter out reads that are over-soft-clipped
PairedReadFilter Filter out unpaired reads
PassesVendorQualityCheckReadFilter Filter out reads failing platfor/vendor quality checks
PlatformReadFilter Keep only reads with matching Read Group platform
PlatformUnitReadFilter Filter out reads with matching platform unit attribute
PrimaryLineReadFilter Keep only reads representing primary alignments (those that satisfy both the NotSecondaryAlignment and NotSupplementaryAlignment filters, or in terms of SAM flag values, must have neither of the 0x100 or 0x800 flags set).
ProperlyPairedReadFilter Keep only reads that are properly paired
ReadGroupBlackListReadFilter Keep records not matching the read group tag and exact match string.
ReadGroupReadFilter Keep only reads from the specified read group
ReadLengthEqualsCigarLengthReadFilter Filter out reads where the read and CIGAR do not match in length
ReadLengthReadFilter Keep only reads whose length is within a certain range
ReadNameReadFilter Keep only reads with this read name
ReadStrandFilter Keep only reads whose strand is as specified
SampleReadFilter Keep only reads for a given sample
SecondOfPairReadFilter Keep only paired reads that are second of pair
SeqIsStoredReadFilter Keep only reads with sequenced bases
SoftClippedReadFilter Filter out reads that are over-soft-clipped
ValidAlignmentEndReadFilter Keep only reads where the read end is properly aligned
ValidAlignmentStartReadFilter Keep only reads with a valid alignment start
WellformedReadFilter Keep only reads that are well-formed

Available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. See

Name Summary
AS_BaseQualityRankSumTest Allele-specific rank sum test of REF versus ALT base quality scores (AS_BaseQRankSum)
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 samples (AS_InbreedingCoeff)
AS_MappingQualityRankSumTest Allele-specific rank sum test for mapping qualities of REF versus ALT reads (AS_MQRankSum)
AS_QualByDepth Allele-specific call confidence normalized by depth of sample reads supporting the allele (AS_QD)
AS_RMSMappingQuality Allele-specific root-mean-square of the mapping quality of reads across all samples (AS_MQ)
AS_ReadPosRankSumTest Allele-specific rank sum test for relative positioning of REF versus ALT allele within reads (AS_ReadPosRankSum)
AS_StrandOddsRatio Allele-specific strand bias estimated by the symmetric odds ratio test (AS_SOR)
AlleleFraction Variant allele fraction for a genotype
BaseQuality Median base quality of bases supporting each allele (MBQ)
BaseQualityRankSumTest Rank sum test of REF versus ALT base quality scores (BaseQRankSum)
ChromosomeCounts Counts and frequency of alleles in called genotypes (AC, AF, AN)
ClippingRankSumTest Rank sum test for hard-clipped bases on REF versus ALT reads (ClippingRankSum)
CountNs Number of Ns at the pileup
Coverage Total depth of coverage per sample and over all samples (DP)
DepthPerAlleleBySample Depth of coverage of each allele per sample (AD)
DepthPerSampleHC Depth of informative coverage for each sample (DP)
ExcessHet Phred-scaled p-value for exact test of excess heterozygosity (ExcessHet)
FisherStrand Strand bias estimated using Fisher's exact test (FS)
FragmentLength Median fragment length of reads supporting each allele (MFRL)
GenotypeSummaries Summary of genotype statistics from all samples (NCC, GQ_MEAN, GQ_STDDEV)
InbreedingCoeff Likelihood-based test for the consanguinity among samples (InbreedingCoeff)
LikelihoodRankSumTest Rank sum test of per-read likelihoods of REF versus ALT reads (LikelihoodRankSum)
MappingQuality Median mapping quality of reads supporting each allele (MMQ)
MappingQualityRankSumTest Rank sum test for mapping qualities of REF versus ALT reads (MQRankSum)
MappingQualityZero Count of all reads with MAPQ = 0 across all samples (MQ0)
OrientationBiasReadCounts Count of read pairs in the F1R2 and F2R1 configurations supporting REF and ALT alleles (F1R2, F2R1)
OriginalAlignment Number of alt reads with an OA tag that doesn't match the current alignment contig.
PossibleDeNovo Existence of a de novo mutation in at least one of the given families (hiConfDeNovo, loConfDeNovo)
QualByDepth Variant confidence normalized by unfiltered depth of variant samples (QD)
RMSMappingQuality Root mean square of the mapping quality of reads across all samples (MQ)
ReadPosRankSumTest Rank sum test for relative positioning of REF versus ALT alleles within reads (ReadPosRankSum)
ReadPosition Median distance of variant starts from ends of reads supporting each allele (MPOS)
ReferenceBases Annotate with local reference bases (REF_BASES)
SampleList List of samples that are not homozygous reference at a variant site (Samples)
StrandBiasBySample Number of forward and reverse reads that support REF and ALT alleles (SB)
StrandOddsRatio Strand bias estimated by the symmetric odds ratio test (SOR)
TandemRepeat Tandem repeat unit composition and counts per allele (STR, RU, RPA)
UniqueAltReadCount Number of non-duplicate-insert ALT reads (UNIQ_ALT_READ_COUNT)

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GATK version built at Wed, 9 Oct 2019 15:19:59 -0400.