jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-4.0.2.1.zip
--2018-08-30 11:47:20-- https://github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-4.0.2.1.zip
Resolving github.com (github.com)... 192.30.253.113, 192.30.253.112
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--2018-08-30 11:47:21-- https://github-production-release-asset-2e65be.s3.amazonaws.com/27452807/b52ea0c4-1e27-11e8-8de3-124a69f123c8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180830%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180830T094721Z&X-Amz-Expires=300&X-Amz-Signature=891dad1fa9f625f83ccfdc7a1fcbf39d4ceecb227a6da4ac5ee61d2945414d7e&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dgatk-4.0.2.1.zip&response-content-type=application%2Foctet-stream
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jitendra@jitendra-UNLOCK-INSTALL[gatk-4.0.2.1] ./gatk []
Usage template for all tools (uses --spark-runner LOCAL when used with a Spark tool)
gatk AnyTool toolArgs
Usage template for Spark tools (will NOT work on non-Spark tools)
gatk SparkTool toolArgs [ -- --spark-runner <LOCAL | SPARK | GCS> sparkArgs ]
Getting help
gatk --list Print the list of available tools
gatk Tool --help Print help on a particular tool
Configuration File Specification
--gatk-config-file PATH/TO/GATK/PROPERTIES/FILE
gatk forwards commands to GATK and adds some sugar for submitting spark jobs
--spark-runner <target> controls how spark tools are run
valid targets are:
LOCAL: run using the in-memory spark runner
SPARK: run using spark-submit on an existing cluster
--spark-master must be specified
--spark-submit-command may be specified to control the Spark submit command
arguments to spark-submit may optionally be specified after --
GCS: run using Google cloud dataproc
commands after the -- will be passed to dataproc
--cluster <your-cluster> must be specified after the --
spark properties and some common spark-submit parameters will be translated
to dataproc equivalents
--dry-run may be specified to output the generated command line without running it
--java-options 'OPTION1[ OPTION2=Y ... ]' optional - pass the given string of options to the
java JVM at runtime.
Java options MUST be passed inside a single string with space-separated values.
jitendra@jitendra-UNLOCK-INSTALL[gatk-4.0.2.1] ./gatk --list []
Using GATK jar /media/jitendra/OSDisk/SNP/gatk-4.0.2.1/gatk-package-4.0.2.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -jar /media/jitendra/OSDisk/SNP/gatk-4.0.2.1/gatk-package-4.0.2.1-local.jar --help
OpenJDK 64-Bit Server VM warning: Insufficient space for shared memory file:
13132
Try using the -Djava.io.tmpdir= option to select an alternate temp location.
USAGE: <program name> [-h]
Available Programs:
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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.
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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
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 Create a VCF given the output of GermlineCNVCaller.
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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
CollectFragmentCounts (BETA Tool) Collects fragment 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
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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) <b>Produces a summary of alignment metrics from a SAM or BAM file.</b>
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) <b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b>
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
FilterLongReadAlignmentsSAMSpark (EXPERIMENTAL Tool) Examines alignments of chimeric contigs, attempting to produce an optimal tiling
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
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
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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.
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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
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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
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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.
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
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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.
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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
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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 complex structural variants
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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 bams 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 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
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.
NeuralNetInference (EXPERIMENTAL Tool) Apply 1d Convolutional Neural Net to filter annotated variants
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
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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
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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
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