Technical Documentation Index

Engine Parameters (available to all tools)

Name	Summary
CommandLineGATK	All command line parameters accepted by all tools in the GATK.

Diagnostics and Quality Control Tools

Name	Summary
BaseCoverageDistribution	Simple walker to plot the coverage distribution per base
CallableLoci	Emits a data file containing information about callable, uncallable, poorly mapped, and other parts of the genome
CheckAlignment	Validates consistency of the aligner interface
CheckPileup	At every locus in the input set, compares the pileup data (reference base, aligned base from each overlapping read, and quality score) to the reference pileup data generated by samtools.
CompareBAM	Given two BAMs with different read groups, it compares them based on ReduceReads metrics.
CompareCallableLoci	Test routine for new VariantContext object
CountBases	Walks over the input data set, calculating the number of bases seen for diagnostic purposes.
CountIntervals	Count contiguous regions in an interval list.
CountLoci	Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.
CountMales	Walks over the input data set, calculating the number of reads seen from male samples for diagnostic purposes.
CountRODs	Prints out counts of the number of reference ordered data objects encountered.
CountRODsByRef	Prints out counts of the number of reference ordered data objects encountered along the reference.
CountReadEvents	Walks over the input data set, counting the number of read events (from the CIGAR operator)
CountReads	Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
CountTerminusEvent	Walks over the input data set, counting the number of reads ending in insertions/deletions or soft-clips
CoveredByNSamplesSites	Print intervals file with all the variant sites for which most of the samples have good coverage
DepthOfCoverage	Toolbox for assessing sequence coverage by a wide array of metrics, partitioned by sample, read group, or library
DiagnoseTargets	Analyzes coverage distribution and validates read mates for a given interval and sample.
DiffObjects	A generic engine for comparing tree-structured objects
ErrorRatePerCycle	Computes the read error rate per position in read (in the original 5'->3' orientation that the read had coming off the machine) Emits a GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate for each read group in the input BAMs FOR ONLY THE FIRST OF PAIR READS.
FastaStats	Calculate basic statistics about the reference sequence itself
FindCoveredIntervals	Outputs a list of intervals that are covered above a given threshold.
FlagStat	A reimplementation of the 'samtools flagstat' subcommand in the GATK
GCContentByInterval	Walks along reference and calculates the GC content for each interval.
Pileup	Emulates the samtools pileup command to print aligned reads
PrintRODs	Prints out all of the RODs in the input data set.
QCRef	Quality control for the reference fasta
ReadClippingStats	Walks over the input reads, printing out statistics about the read length, number of clipping events, and length of the clipping to the output stream.
ReadGroupProperties	Emits a GATKReport containing read group, sample, library, platform, center, sequencing data, paired end status, simple read type name (e.g.
ReadLengthDistribution	Outputs the read lengths of all the reads in a file.
RecalibrationPerformance	Evaluate the performance of the base recalibration process

Sequence Data Processing Tools

Name	Summary
BaseRecalibrator	First pass of the base quality score recalibration -- Generates recalibration table based on various user-specified covariates (such as read group, reported quality score, machine cycle, and nucleotide context).
ClipReads	This tool provides simple, powerful read clipping capabilities to remove low quality strings of bases, sections of reads, and reads containing user-provided sequences.
IndelRealigner	Performs local realignment of reads to correct misalignments due to the presence of indels.
LeftAlignIndels	Left-aligns indels from reads in a bam file.
PrintReads	Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear in the input file.
ReadAdaptorTrimmer	Utility tool to blindly strip base adaptors.
RealignerTargetCreator	Emits intervals for the Local Indel Realigner to target for realignment.
ReduceReads	Reduces the BAM file using read based compression that keeps only essential information for variant calling
SplitSamFile	Divides the input data set into separate BAM files, one for each sample in the input data set.

Variant Discovery Tools

Name	Summary
ApplyRecalibration	Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel truth sensitivity levels which were specified during VariantRecalibration
BeagleOutputToVCF	Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
GATKPaperGenotyper	A simple Bayesian genotyper, that outputs a text based call format.
HaplotypeCaller	Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region.
PhaseByTransmission	Computes the most likely genotype combination and phases trios and parent/child pairs
ProduceBeagleInput	Converts the input VCF into a format accepted by the Beagle imputation/analysis program.
ReadBackedPhasing	Walks along all variant ROD loci, caching a user-defined window of VariantContext sites, and then finishes phasing them when they go out of range (using upstream and downstream reads).
UnifiedGenotyper	A variant caller which unifies the approaches of several disparate callers -- Works for single-sample and multi-sample data.
VariantRecalibrator	Create a Gaussian mixture model by looking at the annotations values over a high quality subset of the input call set and then evaluate all input variants.
VariantsToBeagleUnphased	Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample in input variant file.

Variant Evaluation and Manipulation Tools

Name	Summary
CatVariants	Concatenates VCF files of non-overlapped genome intervals, all with the same set of samples
CombineVariants	Combines VCF records from different sources.
FilterLiftedVariants	Filters a lifted-over VCF file for ref bases that have been changed.
GenotypeConcordance	Genotype concordance (per-sample and aggregate counts and frequencies, NRD/NRS and site allele overlaps) between two callsets
HaplotypeResolver	Haplotype-based resolution of variants in 2 different eval files.
LeftAlignAndTrimVariants	Left-aligns indels from a variants file.
LiftoverVariants	Lifts a VCF file over from one build to another.
RandomlySplitVariants	Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.
RegenotypeVariants	Regenotypes the variants from a VCF.
SelectHeaders	Selects headers from a VCF source.
SelectVariants	Selects variants from a VCF source.
VariantAnnotator	Annotates variant calls with context information.
VariantEval	General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
VariantFiltration	Filters variant calls using a number of user-selectable, parameterizable criteria.
VariantsToAllelicPrimitives	Takes alleles from a variants file and breaks them up (if possible) into more basic/primitive alleles.
VariantsToBinaryPed	Converts a VCF file to a binary plink Ped file (.bed/.bim/.fam)
VariantsToTable	Emits specific fields from a VCF file to a tab-deliminated table
VariantsToVCF	Converts variants from other file formats to VCF format.

Help Utilities

Name	Summary
ListAnnotations	Utility program to print a list of available annotations

Reference Utilities

Name	Summary
FastaAlternateReferenceMaker	Generates an alternative reference sequence over the specified interval.
FastaReferenceMaker	Renders a new reference in FASTA format consisting of only those loci provided in the input data set.

Validation Utilities

Name	Summary
GenotypeAndValidate	Genotypes a dataset and validates the calls of another dataset using the Unified Genotyper.
ValidateVariants	Validates a VCF file with an extra strict set of criteria.
ValidationAmplicons	Creates FASTA sequences for use in Seqenom or PCR utilities for site amplification and subsequent validation
ValidationSiteSelector	Randomly selects VCF records according to specified options.
VariantValidationAssessor	Annotates a validation (from Sequenom for example) VCF with QC metrics (HW-equilibrium, % failed probes)

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.
DuplicateReadFilter	Filter out duplicate reads.
FailsVendorQualityCheckFilter	Filter out reads that fail the vendor quality check.
HCMappingQualityFilter	Filter out reads with low mapping qualities.
MalformedReadFilter	Filter out malformed reads.
MappingQualityFilter	Filter out reads with low mapping qualities.
MappingQualityUnavailableFilter	Filter out mapping quality zero reads.
MappingQualityZeroFilter	Filter out mapping quality zero reads.
MateSameStrandFilter	Filter out reads that are not paired, have their mate unmapped, are duplicates, fail vendor quality check or both mate and read are in the same strand.
MaxInsertSizeFilter	Filter out reads that exceed a given max insert size
MissingReadGroupFilter	Filter out reads without read groups.
NoOriginalQualityScoresFilter	Filter out reads that don't have base an original quality quality score tag (usually added by BQSR)
NotPrimaryAlignmentFilter	Filter out duplicate reads.
Platform454Filter	Filter out 454 reads.
PlatformFilter	Filter out PL matching reads.
PlatformUnitFilter	Filter out reads that have blacklisted platform unit tags.
ReadGroupBlackListFilter	Removes records matching the read group tag and exact match string.
ReadLengthFilter	Filters out reads whose length is >= some value or < some value.
ReadNameFilter	Filter out all reads except those with this read name
ReadStrandFilter	Filters out reads whose strand is negative or positive
ReassignMappingQualityFilter	A read filter (transformer) that sets all reads mapping quality to a given value.
ReassignOneMappingQualityFilter	A read filter (transformer) that changes a given read mapping quality to a different value.
SampleFilter	Filter out all reads except those with this sample
SingleReadGroupFilter	Only use reads from the specified read group.
UnmappedReadFilter	Filter out unmapped reads.

ROD Codecs

Tribble codecs for reading reference ordered data (ROD) files such as VCF or 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

Uncategorized

Name	Summary
AssessReducedQuals	Emits intervals in which the differences between the original and reduced bam quals are bigger epsilon (unless the quals of the reduced bam are above sufficient threshold)
DownsampleReadsQC

User Exceptions

Errors caused by incorrect user behavior, such as bad files, bad arguments, etc.

Name	Summary
ArgumentException	Generic class for handling misc parsing exceptions.
ArgumentsAreMutuallyExclusiveException	An exception indicating that mutually exclusive options have been passed in the same command line.
DynamicClassResolutionException	Class for handling common failures of dynamic class resolution User: depristo Date: Sep 3, 2010 Time: 2:24:09 PM
InvalidArgumentException	An exception for undefined arguments.
InvalidArgumentValueException	An exception for values whose format is invalid.
MissingArgumentException	An exception indicating that some required arguments are missing.
MissingArgumentValueException	Specifies that a value was missing when attempting to populate an argument.
TooManyValuesForArgumentException	An exception indicating that too many values have been provided for the given argument.
UnknownEnumeratedValueException	An exception for when an argument doesn't match an of the enumerated options for that var type
UnmatchedArgumentException	An exception for values that can't be mated with any argument.
UserException	Represents the common user errors detected by Sting / GATK Root class for all GATK user errors, as well as the container for errors themselves User: depristo Date: Sep 3, 2010 Time: 2:24:09 PM

Variant Annotations

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

Name	Summary
AlleleBalance	The allele balance (fraction of ref bases over ref + alt bases) across all biallelic het-called samples
AlleleBalanceBySample	Allele balance per sample
BaseCounts	Count of A, C, G, T bases across all samples
BaseQualityRankSumTest	U-based z-approximation from the Mann-Whitney Rank Sum Test for base qualities
ChromosomeCounts	Allele counts and frequency for each ALT allele and total number of alleles in called genotypes
ClippingRankSumTest	U-based z-approximation from the Mann-Whitney Rank Sum Test for reads with clipped bases
Coverage	Total (unfiltered) depth over all samples.
DepthPerAlleleBySample	The depth of coverage of each allele per sample
FisherStrand	Phred-scaled p-value using Fisher's Exact Test to detect strand bias
GCContent	GC content of the reference around the given site
HaplotypeScore	Consistency of the site with two (and only two) segregating haplotypes.
HardyWeinberg	Hardy-Weinberg test for disequilibrium
HomopolymerRun	Largest contiguous homopolymer run of the variant allele
InbreedingCoeff	Likelihood-based (using PL field) test for the inbreeding among samples.
LowMQ	Triplet annotation: fraction of MAQP == 0, MAPQ < 10, and count of all mapped reads
MVLikelihoodRatio	Likelihood of being a Mendelian Violation
MappingQualityRankSumTest	U-based z-approximation from the Mann-Whitney Rank Sum Test for mapping qualities
MappingQualityZero	Total count across all samples of mapping quality zero reads
MappingQualityZeroBySample	Count for each sample of mapping quality zero reads
NBaseCount	The number of N bases, counting only SOLiD data
QualByDepth	Variant confidence (from the QUAL field) / unfiltered depth of non-reference samples.
RMSMappingQuality	Root Mean Square of the mapping quality of the reads across all samples.
ReadPosRankSumTest	U-based z-approximation from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele
SampleList	List all of the polymorphic samples.
SnpEff	A set of genomic annotations based on the output of the SnpEff variant effect predictor tool
SpanningDeletions	Fraction of reads containing spanning deletions at this site
TandemRepeatAnnotator	Annotates variants that are composed of tandem repeats
TransmissionDisequilibriumTest	Wittkowski transmission disequilibrium test
VariantType	Assigns a roughly correct category of the variant type (SNP, MNP, insertion, deletion, etc.)

Technical Documentation Index 2.5-2-gdb4546e