BOL: Downloading GATK !

BioScripts
Jit
Downloading GATK !
Downloading GATK !

By Jit 2067 days ago
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
Connecting to github.com (github.com)|192.30.253.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: 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 [following]
--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
Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.227.56
Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.227.56|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 346889796 (331M) [application/octet-stream]
Saving to: ‘gatk-4.0.2.1.zip’

gatk-4.0.2.1.zip    100%[===================>] 330,82M  8,66MB/s    in 1m 41s  

2018-08-30 11:49:03 (3,27 MB/s) - ‘gatk-4.0.2.1.zip’ saved [346889796/346889796]

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:
--------------------------------------------------------------------------------------
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
    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.

--------------------------------------------------------------------------------------
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

--------------------------------------------------------------------------------------
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

--------------------------------------------------------------------------------------
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.
    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 complex structural variants

--------------------------------------------------------------------------------------
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

--------------------------------------------------------------------------------------
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

--------------------------------------------------------------------------------------
BOL

Jit

Our Sponsors

Downloading GATK !
