Engine Parameters (available to all tools)

Name	Summary
CommandLineGATK	Command line parameters accepted by most if not all tools in the GATK

Diagnostics and Quality Control Tools

Name	Summary
ASEReadCounter	Calculate read counts per allele for allele-specific expression analysis
AnalyzeCovariates	Create plots to visualize base recalibration results
CallableLoci	Collect statistics on callable, uncallable, poorly mapped, and other parts of the genome
CheckPileup	Compare GATK's internal pileup to a reference Samtools pileup
CompareCallableLoci	Compare callability statistics
ContEst	Estimate cross-sample contamination
CountBases	Count the number of bases in a set of reads
CountIntervals	Count contiguous regions in an interval list
CountLoci	Count the total number of covered loci
CountMales	Count the number of reads seen from male samples
CountRODs	Count the number of ROD objects encountered
CountRODsByRef	Count the number of ROD objects encountered along the reference
CountReadEvents	Count the number of read events
CountReads	Count the number of reads
CountTerminusEvent	Count the number of reads ending in insertions, deletions or soft-clips
DepthOfCoverage	Assess sequence coverage by a wide array of metrics, partitioned by sample, read group, or library
DiagnoseTargets	Analyze coverage distribution and validate read mates per interval and per sample
DiffObjects	A generic engine for comparing tree-structured objects
ErrorRatePerCycle	Compute the read error rate per position
FastaStats	Calculate basic statistics about the reference sequence itself
FindCoveredIntervals	Outputs a list of intervals that are covered to or above a given threshold
FlagStat	Collect statistics about sequence reads based on their SAM flags
GCContentByInterval	Calculates the GC content of the reference sequence for each interval
GatherBqsrReports	Gather recalibration reports from parallelized base recalibration runs This tool is intended to be used to combine recalibration tables from runs of BaseRecalibrator parallelized per-interval.
Pileup	Print read alignments in Pileup-style format
PrintRODs	Print out all of the RODs in the input data set
QualifyMissingIntervals	Collect quality metrics for a set of intervals
ReadClippingStats	Collect read clipping statistics
ReadGroupProperties	Collect statistics about read groups and their properties
ReadLengthDistribution	Collect read length statistics
SimulateReadsForVariants	Generate simulated reads for variants

Sequence Data Processing Tools

Name	Summary
BaseRecalibrator	Detect systematic errors in base quality scores
ClipReads	Read clipping based on quality, position or sequence matching
IndelRealigner	Perform local realignment of reads around indels
LeftAlignIndels	Left-align indels within reads in a bam file
PrintReads	Write out sequence read data (for filtering, merging, subsetting etc)
RealignerTargetCreator	Define intervals to target for local realignment
SplitNCigarReads	Splits reads that contain Ns in their CIGAR string
SplitSamFile	Split a BAM file by sample

Variant Discovery Tools

Name	Summary
ApplyRecalibration	Apply a score cutoff to filter variants based on a recalibration table
CalculateGenotypePosteriors	Calculate genotype posterior likelihoods given panel data
GATKPaperGenotyper	Simple Bayesian genotyper used in the original GATK paper
GenotypeGVCFs	Perform joint genotyping on gVCF files produced by HaplotypeCaller
HaplotypeCaller	Call germline SNPs and indels via local re-assembly of haplotypes
MuTect2	Call somatic SNPs and indels via local re-assembly of haplotypes
RegenotypeVariants	Regenotypes the variants from a VCF containing PLs or GLs.
UnifiedGenotyper	Call SNPs and indels on a per-locus basis
VariantRecalibrator	Build a recalibration model to score variant quality for filtering purposes

Variant Evaluation Tools

Name	Summary
GenotypeConcordance	Genotype concordance between two callsets
ValidateVariants	Validate a VCF file with an extra strict set of criteria
VariantEval	General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
VariantFiltration	Filter variant calls based on INFO and FORMAT annotations

Variant Manipulation Tools

Name	Summary
CatVariants	Concatenate VCF files of non-overlapping genome intervals, all with the same set of samples
CombineGVCFs	Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
CombineVariants	Combine variant records from different sources
HaplotypeResolver	Haplotype-based resolution of variants in separate callsets.
LeftAlignAndTrimVariants	Left-align indels in a variant callset
PhaseByTransmission	Compute the most likely genotype combination and phasing for trios and parent/child pairs
RandomlySplitVariants	Randomly split variants into different sets
ReadBackedPhasing	Annotate physical phasing information
SelectHeaders	Selects headers from a VCF source
SelectVariants	Select a subset of variants from a larger callset
ValidationSiteSelector	Randomly select variant records according to specified options
VariantAnnotator	Annotate variant calls with context information
VariantsToAllelicPrimitives	Simplify multi-nucleotide variants (MNPs) into more basic/primitive alleles.
VariantsToBinaryPed	Convert VCF to binary pedigree file
VariantsToTable	Extract specific fields from a VCF file to a tab-delimited table
VariantsToVCF	Convert variants from other file formats to VCF format

Annotation Modules

Annotations available to VariantAnnotator and the variant callers (some restrictions apply)

Name	Summary
AS_BaseQualityRankSumTest	Allele-specific rank Sum Test of REF versus ALT base quality scores
AS_FisherStrand	Allele-specific strand bias estimated using Fisher's Exact Test *
AS_InbreedingCoeff	Allele-specific likelihood-based test for the inbreeding among samples
AS_InsertSizeRankSum	Allele specific Rank Sum Test for insert sizes of REF versus ALT reads
AS_MQMateRankSumTest	Allele specific Rank Sum Test for mate's mapping qualities of REF versus ALT reads
AS_MappingQualityRankSumTest	Allele specific Rank Sum Test for mapping qualities of REF versus ALT reads
AS_QualByDepth	Allele-specific call confidence normalized by depth of sample reads supporting the allele
AS_RMSMappingQuality	Allele-specific Root Mean Square of the mapping quality of reads across all samples.
AS_ReadPosRankSumTest	Allele-specific Rank Sum Test for relative positioning of REF versus ALT allele within reads
AS_StrandOddsRatio	Allele-specific strand bias estimated by the Symmetric Odds Ratio test
AlleleBalance	Allele balance across all samples
AlleleBalanceBySample	Allele balance per sample
AlleleCountBySample	Allele count and frequency expectation per sample
BaseCounts	Count of A, C, G, T bases across all samples
BaseCountsBySample	Count of A, C, G, T bases for each sample
BaseQualityRankSumTest	Rank Sum Test of REF versus ALT base quality scores
BaseQualitySumPerAlleleBySample	Sum of evidence in reads supporting each allele for each sample
ChromosomeCounts	Counts and frequency of alleles in called genotypes
ClippingRankSumTest	Rank Sum Test for hard-clipped bases on REF versus ALT reads
ClusteredReadPosition	Detect clustering of variants near the ends of reads
Coverage	Total depth of coverage per sample and over all samples.
DepthPerAlleleBySample	Depth of coverage of each allele per sample
DepthPerSampleHC	Depth of informative coverage for each sample.
ExcessHet	Phred-scaled p-value for exact test of excess heterozygosity
FisherStrand	Strand bias estimated using Fisher's Exact Test
FractionInformativeReads	The fraction of reads deemed informative over the entire cohort
GCContent	GC content of the reference around the given site
GenotypeSummaries	Summarize genotype statistics from all samples at the site level
HaplotypeScore	Consistency of the site with strictly two segregating haplotypes
HardyWeinberg	Hardy-Weinberg test for transmission disequilibrium
HomopolymerRun	Largest contiguous homopolymer run of the variant allele
InbreedingCoeff	Likelihood-based test for the inbreeding among samples
LikelihoodRankSumTest	Rank Sum Test of per-read likelihoods of REF versus ALT reads
LowMQ	Proportion of low quality reads
MVLikelihoodRatio	Likelihood of being a Mendelian Violation
MappingQualityRankSumTest	Rank Sum Test for mapping qualities of REF versus ALT reads
MappingQualityZero	Count of all reads with MAPQ = 0 across all samples
MappingQualityZeroBySample	Count of reads with mapping quality zero for each sample
NBaseCount	Percentage of N bases
OxoGReadCounts	Count of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate alleles
PossibleDeNovo	Existence of a de novo mutation in at least one of the given families
QualByDepth	Variant call confidence normalized by depth of sample reads supporting a variant
RMSMappingQuality	Root Mean Square of the mapping quality of reads across all samples.
ReadPosRankSumTest	Rank Sum Test for relative positioning of REF versus ALT alleles within reads
SampleList	List samples that are non-reference at a given site
SnpEff	Top effect from SnpEff functional predictions
SpanningDeletions	Fraction of reads containing spanning deletions
StrandAlleleCountsBySample	Number of forward and reverse reads that support each allele
StrandBiasBySample	Number of forward and reverse reads that support REF and ALT alleles
StrandOddsRatio	Strand bias estimated by the Symmetric Odds Ratio test
TandemRepeatAnnotator	Tandem repeat unit composition and counts per allele
TransmissionDisequilibriumTest	Wittkowski transmission disequilibrium test
VariantType	General category of variant

Read Filters

GATK Engine arguments that filter or transfer incoming SAM/BAM data files

Name	Summary
BadCigarFilter	Filter out reads with wonky CIGAR strings
BadMateFilter	Filter out reads whose mate maps to a different contig
CountingFilteringIterator.CountingReadFilter
DuplicateReadFilter	Filter out duplicate reads
FailsVendorQualityCheckFilter	Filter out reads that fail the vendor quality check
HCMappingQualityFilter	Filter out reads with low mapping qualities for HaplotypeCaller
LibraryReadFilter	Only use reads from the specified library
MalformedReadFilter	Filter out malformed reads
MappingQualityFilter	Filter out reads with low mapping qualities
MappingQualityUnavailableFilter	Filter out reads with no mapping quality information
MappingQualityZeroFilter	Filter out reads with mapping quality zero
MateSameStrandFilter	Filter out reads with bad pairing (and related) properties
MaxInsertSizeFilter	Filter out reads that exceed a given insert size
MissingReadGroupFilter	Filter out reads without read group information
NoOriginalQualityScoresFilter	Filter out reads that do not have an original quality quality score (OQ) tag
NotPrimaryAlignmentFilter	Filter out read records that are secondary alignments
OverclippedReadFilter	Filter out reads that are over-soft-clipped
Platform454Filter	Filter out reads produced by 454 technology
PlatformFilter	Filter out reads that were generated by a specific sequencing platform
PlatformUnitFilter	Filter out reads with blacklisted platform unit tags
ReadGroupBlackListFilter	Filter out reads matching a read group tag value
ReadLengthFilter	Filter out reads based on length
ReadNameFilter	Only use reads with this read name
ReadStrandFilter	Filter out reads based on strand orientation
ReassignMappingQualityFilter	Set the mapping quality of all reads to a given value
ReassignOneMappingQualityFilter	Set the mapping quality of reads with a given value to another given value
ReassignOriginalMQAfterIndelRealignmentFilter	Revert the MQ of reads that were modified by IndelRealigner
SampleFilter	Only use reads belonging to a specific sample
SingleReadGroupFilter	Only use reads from the specified read group
UnmappedReadFilter	Filter out unmapped reads

Resource File Codecs

Codecs for reading resource files in reference ordered data (ROD) files such as BED

Name	Summary
BeagleCodec	Codec for Beagle imputation engine
BedTableCodec	The standard table codec that expects loci as contig start stop, not contig:start-stop
RawHapMapCodec	A codec for the file types produced by the HapMap consortium
RefSeqCodec	Allows for reading in RefSeq information
SAMPileupCodec	Decoder for SAM pileup data
SAMReadCodec	Decodes a simple SAM text string
TableCodec	Reads tab deliminated tabular text files

Reference Utilities

Name	Summary
FastaAlternateReferenceMaker	Generate an alternative reference sequence over the specified interval
FastaReferenceMaker	Create a subset of a FASTA reference sequence
QCRef	Quality control for the reference fasta

Tool Documentation Index