Copy Number Variant Discovery

Tools that analyze read coverage to detect copy number variants.

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

Coverage Analysis

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
CollectAllelicCounts	BETA Collects reference and alternate allele counts at specified sites
CollectReadCounts	BETA Collects read counts at specified intervals
CountBases	Count bases in a SAM/BAM/CRAM file
CountBasesSpark	BETA Counts bases in the input SAM/BAM
CountReads	Count reads in a SAM/BAM/CRAM file
CountReadsSpark	BETA 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

Diagnostics and Quality Control

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
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.
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
CrosscheckReadGroupFingerprints (Picard)	DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups appear to 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	BETA 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

Intervals Manipulation

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	BETA Prepares bins for coverage collection
SplitIntervals	Split intervals into sub-interval files.

Metagenomics

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

Other

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	EXPERIMENTAL Condenses homRef blocks in a single-sample GVCF

Read Data Manipulation

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

Name	Summary
AddCommentsToBam (Picard)	Adds comments to the header of a BAM file.
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	BETA 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	BETA 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.
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

Reference

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
CreateSequenceDictionary (Picard)	Creates a sequence dictionary for a reference sequence.
ExtractSequences (Picard)	Subsets intervals from a reference sequence to a new 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.

Short Variant Discovery

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
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 Takes unaligned or aligned reads and runs BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller to generate a VCF file of variants

Structural Variant Discovery

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

Variant Evaluation and Refinement

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

Name	Summary
AnnotatePairOrientation	BETA (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	BETA 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
Funcotator	BETA Functional Annotator
FuncotatorDataSourceDownloader	BETA Data source downloader for Funcotator.
GenotypeConcordance (Picard)	Calculates the concordance between genotype data of one samples in each of two VCFs - one being considered the truth (or reference) the other being the call. The concordance is broken into separate results sections for SNPs and indels. Statistics are reported in three different files.
ValidateBasicSomaticShortMutations	EXPERIMENTAL Check the variants in a VCF against a tumor-normal pair of bams representing the same samples, though not the ones from the actual calls.
ValidateVariants	Validate VCF
VariantsToTable	Extract fields from a VCF file to a tab-delimited table

Variant Filtering

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	EXPERIMENTAL 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	EXPERIMENTAL 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

Variant Manipulation

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	BETA 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.
VcfFormatConverter (Picard)	Converts VCF to BCF or BCF to VCF.
VcfToIntervalList (Picard)	Converts a VCF or BCF file to a Picard Interval List

Base Calling

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.

Read Filters

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
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
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
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

Variant Annotations

Available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. See https://software.broadinstitute.org/gatk/documentation/article?id=10836

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)
OriginalAlignment	Number of alt reads with an OA tag that doesn't match the current alignment contig.
OxoGReadCounts	Count of read pairs in the F1R2 and F2R1 configurations supporting REF and ALT alleles (F1R2, F2R1)
PolymorphicNuMT	Number of alts indicates it could be an autosomal false positive.
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)
StrandArtifact	Annotations for strand artifact filter (SA_POST_PROB, SA_MAP_AF)
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)

Tool Documentation Index