GATK4

[davebx]

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

• 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.

Copy Number Variant Discovery: Tools that analyze read coverage to detect copy number variants.

• AnnotateIntervals (BETA Tool) Annotates intervals with GC content
• CallCopyRatioSegments (BETA Tool) Calls copy-ratio segments as amplified, deleted, or copy-number neutral
• CombineSegmentBreakpoints (EXPERIMENTAL Tool) Combine the breakpoints of two segment files and annotate the resulting intervals with chosen columns from each file.
• CreateReadCountPanelOfNormals (BETA Tool) Creates a panel of normals for read-count denoising
• DenoiseReadCounts (BETA Tool) Denoises read counts to produce denoised copy ratios
• DetermineGermlineContigPloidy (BETA Tool) Determines the baseline contig ploidy for germline samples given counts data
• GermlineCNVCaller (BETA Tool) Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy
• MergeAnnotatedRegions (EXPERIMENTAL Tool) (EXPERIMENTAL) Merge annotated genomic regions based entirely on contig and annotation value.
• ModelSegments (BETA Tool) Models segmented copy ratios from denoised read counts and segmented minor-allele fractions from allelic counts
• PlotDenoisedCopyRatios (BETA Tool) Creates plots of denoised copy ratios
• PlotModeledSegments (BETA Tool) Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates
• PostprocessGermlineCNVCalls (BETA Tool) Postprocesses the output of GermlineCNVCaller and generates VCF files.
• TagGermlineEvents (EXPERIMENTAL Tool) (EXPERIMENTAL) Do a simplistic tagging of germline events in a tumor segment file.

Coverage Analysis: Tools that count coverage, e.g. depth per allele

• ASEReadCounter Generates table of filtered base counts at het sites for allele specific expression
• CollectAllelicCounts (BETA Tool) Collects reference and alternate allele counts at specified sites
• CollectReadCounts (BETA Tool) Collects read counts at specified intervals
• CountBases Count bases in a SAM/BAM/CRAM file
• CountBasesSpark (BETA Tool) Counts bases in the input SAM/BAM
• CountReads Count reads in a SAM/BAM/CRAM file
• CountReadsSpark (BETA Tool) Counts reads in the input SAM/BAM
• GetPileupSummaries (BETA Tool) Tabulates pileup metrics for inferring contamination
• Pileup Prints read alignments in samtools pileup format
• PileupSpark (BETA Tool) Prints read alignments in samtools pileup format

Diagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics

• 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 Tool) (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 Tool) 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) (BETA Tool) (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 Tool) Collects insert size distribution information on alignment data
• CollectJumpingLibraryMetrics (Picard) Collect jumping library metrics.
• CollectMultipleMetrics (Picard) Collect multiple classes of metrics.
• CollectMultipleMetricsSpark (BETA Tool) 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 Tool) 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)(BETA Tool) (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 Tool) 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.
• EstimateLibraryComplexityGATK (BETA Tool) Estimate library complexity from the sequence of read pairs
• FlagStat Accumulate flag statistics given a BAM file
• FlagStatSpark (BETA Tool) Spark tool to accumulate flag statistics
• GetSampleName (BETA Tool) Emit a single sample name
• IdentifyContaminant (Picard) Computes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.
• MeanQualityByCycle (Picard) Collect mean quality by cycle.
• MeanQualityByCycleSpark (BETA Tool) MeanQualityByCycle on Spark
• QualityScoreDistribution (Picard) Chart the distribution of quality scores.
• QualityScoreDistributionSpark (BETA Tool) 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

• 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 Tool) 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

• 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

• CreateHadoopBamSplittingIndex (BETA Tool) 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.
• GatherBQSRReports Gathers scattered BQSR recalibration reports into a single file
• GatherTranches (BETA Tool) Gathers scattered VQSLOD tranches into a single file
• IndexFeatureFile Creates an index for a feature file, e.g. VCF or BED file.
• ParallelCopyGCSDirectoryIntoHDFSSpark (BETA Tool) Parallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark

Read Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format

• 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 Tool) Apply base quality score recalibration on Spark
• BQSRPipelineSpark (BETA Tool) 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 Tool) Generate recalibration table for Base Quality Score Recalibration (BQSR) on Spark
• BaseRecalibratorSparkSharded (EXPERIMENTAL Tool) BaseRecalibrator on Spark (experimental sharded implementation)
• BuildBamIndex (Picard) Generates a BAM index ".bai" file.
• BwaAndMarkDuplicatesPipelineSpark (BETA Tool) Takes name-sorted file and runs BWA and MarkDuplicates.
• BwaSpark (BETA Tool) 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 Tool) Convert a headerless BAM shard into a readable BAM
• DownsampleSam (Picard) Downsample a SAM or BAM file.
• ExtractOriginalAlignmentRecordsByNameSpark (BETA Tool) 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.
• MarkDuplicatesGATK (EXPERIMENTAL Tool) Examines aligned records in the supplied SAM/BAM/CRAM file to locate duplicate molecules.
• MarkDuplicatesSpark (BETA Tool) 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 Tool) 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.
• SamToFastqWithTags (Picard) Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags.
• SetNmAndUqTags (Picard) DEPRECATED: Use SetNmMdAndUqTags instead.
• SetNmMdAndUqTags (Picard) Fixes the NM, MD, and UQ tags in a SAM file
• SimpleMarkDuplicatesWithMateCigar (Picard) (BETA Tool) (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 Tool) 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) (BETA Tool) 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

• 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 Tool) 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)

• 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 Tool) HaplotypeCaller on Spark
• Mutect2 Call somatic SNVs and indels via local assembly of haplotypes
• ReadsPipelineSpark (BETA Tool) 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

• DiscoverVariantsFromContigAlignmentsSAMSpark (BETA Tool) (Internal) Examines aligned contigs from local assemblies and calls structural variants
• ExtractSVEvidenceSpark (BETA Tool) (Internal) Extracts evidence of structural variations from reads
• FindBreakpointEvidenceSpark (BETA Tool) (Internal) Produces local assemblies of genomic regions that may harbor structural variants
• StructuralVariationDiscoveryPipelineSpark (BETA Tool) Runs the structural variation discovery workflow on a single sample
• SvDiscoverFromLocalAssemblyContigAlignmentsSpark (BETA Tool) (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

• AnnotatePairOrientation (BETA Tool) (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
• CNNScoreVariants (EXPERIMENTAL Tool) Apply a Convolutional Neural Net to filter annotated variants
• CNNVariantTrain (EXPERIMENTAL Tool) Train a CNN model for filtering variants
• CNNVariantWriteTensors (EXPERIMENTAL Tool) Write variant tensors for training a CNN to filter variants
• 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 Tool) Evaluate concordance of an input VCF against a validated truth VCF
• CountFalsePositives (BETA Tool) Count PASS variants
• CountVariants Counts variant records in a VCF file, regardless of filter status.
• CountVariantsSpark (BETA Tool) CountVariants on Spark
• FilterVariantTranches (EXPERIMENTAL Tool) Apply tranche filtering
• FindMendelianViolations (Picard) Finds mendelian violations of all types within a VCF
• Funcotator (BETA Tool) Functional Annotator
• 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 Tool) 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

• ApplyVQSR Apply a score cutoff to filter variants based on a recalibration table
• CreateSomaticPanelOfNormals (BETA Tool) Make a panel of normals for use with Mutect2
• FilterByOrientationBias (EXPERIMENTAL Tool) Filter Mutect2 somatic variant calls using orientation bias
• FilterMutectCalls Filter somatic SNVs and indels called by Mutect2
• 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

• 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 Tool) Gathers multiple VCF files from a scatter operation into a single VCF file
• 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 Tool) 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) 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