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Tools to analyze copy number data.

Name Summary
AllelicCNV Detect copy-number events using allelic-count data and GATK CNV output
AnnotateTargets Annotate targets with various properties, such as GC content
CalculateTargetCoverage Count overlapping reads target by target
CallSegments Call segments as amplified, deleted, or copy number neutral
CollectAllelicCounts Collects ref/alt counts at sites
CombineReadCounts Combine read Counts
ConvertACNVResults **BETA** (Experimental) Convert AllelicCNV (ACNV) results to Broad CGA Allelic CapSeg (ACS) and TITAN files.
ConvertBedToTargetFile Convert BED to target file
ConvertGSVariantsToSegments (Internal) Convert Genome STRiP VCF file into a segment file
CorrectGCBias Correct for sample-specific GC bias
CreateAllelicPanelOfNormals **BETA** (Experimental) Creates an allelic panel of normals
CreatePanelOfNormals Create a coverage panel of normals
EvaluateCopyNumberTriStateCalls (Internal) Evaluate a set of germline call segments
GermlineCNVCaller **BETA** Performs coverage profile modelling, denoising, and detecting germline copy number variation
GetBayesianHetCoverage Calls heterozygous SNPs, counts ref and alt alleles and gives genotype likelihoods
GetHetCoverage Output ref/alt counts at heterozygous SNPs in normal sample (and at same sites in tumor sample, if specified)
NormalizeSomaticReadCounts Normalize proportional coverage (PCOV) read counts using a panel of normals
PadTargets Create a new target file with padded targets
PerformAlleleFractionSegmentation **BETA** (Experimental) Segment genomic data into regions of constant minor allele fraction
PerformCopyRatioSegmentation **BETA** (Experimental) Segment genomic data into regions of constant copy ratio
PerformJointSegmentation **BETA** (Experimental) Segment genomic data into regions of constant copy ratio and allele fraction
PerformSegmentation Segment genomic data into regions of constant copy-ratio
PlotACNVResults Create plots of denoised and segmented copy-ratio and minor-allele-fraction estimates.
PlotSegmentedCopyRatio Create plots of denoised and segmented copy ratio
SparkGenomeReadCounts Calculate coverage on a WGS bam file using Spark
TargetCoverageSexGenotyper **BETA** Infers sample sex genotypes from raw read counts.
XHMMSegmentCaller (Internal) Discover possible locations of copy number variation
XHMMSegmentGenotyper (Internal) Genotype location for copy number variation

Tools for Diagnostics and Quality Control

Name Summary
AnalyzeCovariates Evaluate and compare base quality score recalibration (BQSR) tables
CheckPileup Compare GATK's internal pileup to a reference Samtools mpileup
Pileup Print read alignments in Pileup-style format

Tools for analysis and manipulation of files in fasta format

Name Summary
CreateSequenceDictionary Creates a dict file from reference sequence in fasta format

Tools for manipulating read-level data (SAM/BAM/CRAM)

Name Summary
ApplyBQSR Apply base quality score recalibration
BaseRecalibrator Generates recalibration table for BQSR
ClipReads Clip reads in a SAM/BAM/CRAM file
CountBases Count bases in a SAM/BAM/CRAM file
CountReads Count reads in a SAM/BAM/CRAM file
FilterReads Creates a new SAM/BAM/CRAM file by including or excluding aligned reads
FlagStat A reimplementation of the 'samtools flagstat' subcommand
GatherBQSRReports Gathers scattered BQSR recalibration reports into a single file
MergeBamAlignment Merges alignment data from a SAM/BAM with data in an unmapped SAM/BAM/CRAM file
MergeSamFiles Merges multiple SAM/BAM files into one file
PrintReads Print reads in the SAM/BAM/CRAM file
ReorderSam Reorders reads in a SAM/BAM file to match ordering in reference
SortSam Sorts a SAM/BAM/CRAM file
SplitReads Outputs reads from a SAM/BAM/CRAM by read group, sample and library name
ValidateSamFile Validates a SAM/BAM/CRAM file

Pipelines that combine tools and use Apache Spark for scaling out (experimental)

Name Summary
BQSRPipelineSpark **BETA** Both steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark
BwaAndMarkDuplicatesPipelineSpark **BETA** Takes name-sorted file and runs BWA and MarkDuplicates.
ReadsPipelineSpark **BETA** Takes aligned reads (likely from BWA) and runs MarkDuplicates, BQSR, and HaplotypeCaller. The final result is analysis-ready variants

Tools that use Apache Spark for scaling out (experimental)

Name Summary
ApplyBQSRSpark **BETA** ApplyBQSR on Spark
BaseRecalibratorSpark **BETA** BaseRecalibrator on Spark
BaseRecalibratorSparkSharded **BETA** BaseRecalibrator on Spark (experimental sharded implementation)
CollectBaseDistributionByCycleSpark **BETA** CollectBaseDistributionByCycle on Spark
CollectInsertSizeMetricsSpark **BETA** Collect Insert Size Distribution on Spark
CollectMultipleMetricsSpark **BETA** A "meta-metrics" calculating program that produces multiple metrics for the provided SAM/BAM/CRAM file
CollectQualityYieldMetricsSpark **BETA** CollectQualityYieldMetrics on Spark
CountBasesSpark **BETA** CountBases on Spark
CountReadsSpark **BETA** CountReads on Spark
CountVariantsSpark **BETA** CountVariants on Spark
CreateHadoopBamSplittingIndex **BETA** create a hadoop-bam splitting index
FlagStatSpark **BETA** FlagStat on Spark
HaplotypeCallerSpark **BETA** HaplotypeCaller on Spark
PileupSpark **BETA** Print read alignments in Pileup-style format on Spark
PrintReadsSpark **BETA** PrintReads on Spark

Tools for manipulating variants and associated metadata

Name Summary
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
ApplyVQSR Apply a score cutoff to filter variants based on a recalibration table
CalculateContamination Calculate the fraction of reads coming from cross-sample contamination
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
CreateSomaticPanelOfNormals **BETA** Make a panel of normals for use with Mutect2
FilterByOrientationBias **BETA** (Experimental) Filter Mutect2 somatic variant calls using orientation bias
FilterMutectCalls **BETA** Filter somatic SNVs and indels called by Mutect2
GatherTranches Gathers scattered VQSLOD tranches into a single file
GenotypeGVCFs Perform joint genotyping on one or more samples pre-called with HaplotypeCaller
GetPileupSummaries **BETA** Calculate pileup statistics for inferring contamination
HaplotypeCaller **BETA** Call germline SNPs and indels via local re-assembly of haplotypes
IndexFeatureFile Creates indices for Feature-containing files (eg VCF and BED files)
Mutect2 **BETA** Call somatic SNVs and indels via local assembly of haplotypes
RemoveNearbyIndels (Internal) Remove indels that are close to each other from a vcf
SelectVariants Select a subset of variants from a VCF file
SplitIntervals Split intervals into sub-interval files.
UpdateVCFSequenceDictionary Updates the sequence dictionary in a variant file.
ValidateVariants Validate VCF
VariantFiltration Filter variant calls based on INFO and FORMAT annotations
VariantRecalibrator Build a recalibration model to score variant quality for filtering purposes
VariantsToTable Extract specific fields from a VCF file to a tab-delimited table

Read Filters used by the engine to select reads to be included for analysis

Name Summary
AlignmentAgreesWithHeaderReadFilter Checks to ensure that the alignment of each read makes sense based on the contents of the header.
AllowAllReadsReadFilter local classes for static read filters
AmbiguousBaseReadFilter Filters out reads with more than a threshold number of N's.
FragmentLengthReadFilter Keep reads that are within a given max fragment length.
LibraryReadFilter Keep only reads from the specified library.
MappingQualityReadFilter Keep reads with mapping qualities within a specified range.
MateDifferentStrandReadFilter Reads that have a mapped mate and both mate and read are on different same strands (ie the usual situation).
MateOnSameContigOrNoMappedMateReadFilter Reads that either have a mate that maps to the same contig, or don't have a mapped mate.
OverclippedReadFilter Filter out reads that are over-soft-clipped
PlatformReadFilter Keep only reads that match th PL attribute.
PlatformUnitReadFilter Keep reads that do not have blacklisted platform unit tags.
ReadGroupBlackListReadFilter Keep records not matching the read group tag and exact match string.
ReadGroupReadFilter Only use reads from the specified read group.
ReadLengthReadFilter Keep only reads whose length is ≥ min value and ≤ max value.
ReadNameReadFilter Keep only reads with this read name.
ReadStrandFilter Keep only reads whose strand is forward or reverse
SampleReadFilter Keep only reads for a given sample.
WellformedReadFilter Tests whether a read is "well-formed" -- that is, is free of major internal inconsistencies and issues that could lead to errors downstream.

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GATK version 4.beta.5-SNAPSHOT built at 13-45-2017 04:45:04.