GATK (全称The Genome Analysis Toolkit)是Broad Institute开发的用于二代重测序数据分析的一款软件，是基因分析的工具集。在4.0以后，GATK包含有Picard工具集，所有Picard工具都能够使用GATK完成。
1.软件运行的要求：
大部分的GATK4工具只需要简单的软件运行条件：Unix-style OS and Java 1.8。但是也有一些哦那个局需要额外的R或Python。有一些工具需要生成图时会用到R(gsalib, ggplot2, reshape, gplots)。gatk-launch 需要用到Python。
2.下载：
从https://github.com/broadinstitute/gatk/releases后加压就是以下几个文件和文件夹：
gatk gatk-package-[version]-local.jar gatk-package-[version]-spark.jar README.md
gatk-package-[version]-local.jar主要是用来运行的jar。至于gatk-package-[version]-spark.jar是spark运行所需。
3.安装：
GATK不需要安装，将gatk文件export PATH=$PATH:/path/to/gatk-package/gatk中，就行。/path/to/gatk-package/gatk就是gatk所在的目录，必须保证gatk和*.jar放在一起。
4.测试运行：
./gatk --help
会输出一系列帮助信息。
5. 运行GATK和Picard命令：
常见的命令按照以下句势：
gatk [--java-options "jvm args like -Xmx4G go here"] 工具名称 [GATK args go here]
例如：
gatk --java-options "-Xmx8G" HaplotypeCaller -R reference.fasta -I input.bam -O output.vcf
简单的Picard命令：
gatk ValidateSamFile -I input.bam -MODE SUMMA
5.1 GATK的命令详细说明：
5.1.1 Java基础命令
GATK也遵循Java的运行模式：
java -jar program.jar [program argument
5.1.2 gatk包装后的客户端命令
如果使用gatk包装后的客户端，那么就不需要使用java的命名了，直接运行
gatk [program arguments]
5.1.3 添加GATK参数
唯一需要的是工具名及工具的命令
gatk ToolName [tool arguments]
再工具名后，需要添加工具命令
gatk ToolName --argument-name value
后面的命令可以使用--，也可以使用-，命令是没有顺序的，如果有二进制的命名是，是需要Flags的，例如 TRUE or FALSE，例如--create-output-variant-index FALSE
5.1.4 添加Java参数
当使用java命名时，需要在java和-jar之间添加。例如使用-Xmx指定需要的内存大小。
java -Xmx4G -jar program.jar [program arguments]
但是如果需要使用gatk的程序命令制定内存大小时，则需要--java-options，例如：
gatk --java-options "-Xmx4G" [program arguments]
但是如果需要使用两个命令时，则可以直接在双引号内加入进去就可以。
gatk --java-options "-Xmx4G -XX:+PrintGCDetails" [program arguments]
5.1.5 添加Spark参数
Apache Spark 是专为大规模数据处理而设计的快速通用的计算引擎。Spark 是一种与 Hadoop 相似的开源集群计算环境，但是两者之间还存在一些不同之处。
不太懂，无法提供更多信息。
5.16 真实举例
可以在一条命令行也可以使用“\”进行分行输入
gatk --java-options "-Xmx4G" HaplotypeCaller \
-R reference.fasta \
-I sample1.bam \
-O variants.g.vcf \
-ERC GVCF
如果是exon测序的话，就需要提供目标区域，这个时候就可以加上一个-L
gatk --java-options "-Xmx4G" HaplotypeCaller \
-R reference.fasta \
-I sample1.bam \
-O variants.g.vcf \
-ERC GVCF \
-L exome_intervals.list
如果reads中存在问题，可以加上--read-filter过滤reads
gatk --java-options "-Xmx4G" HaplotypeCaller \
-R reference.fasta \
-I sample1.bam \
-O variants.g.vcf \
-ERC GVCF \
-L exome_intervals.list \
--read-filter OverclippedReadFilter
如果想减少运行结果信息，加上 --QUIET
gatk --java-options "-Xmx4G" HaplotypeCaller \
-R reference.fasta \
-I sample1.bam \
-O variants.g.vcf \
-ERC GVCF \
-L exome_intervals.list \
--read-filter OverclippedReadFilter \
--QUIET
如果想关闭automatic variant index生成，
gatk --java-options "-Xmx4G" HaplotypeCaller \
-R reference.fasta \
-I sample1.bam \
-O variants.g.vcf \
-ERC GVCF \
-L exome_intervals.list \
--read-filter OverclippedReadFilter \
--QUIET \
--create-output-variant-index FALSE
工具目录
Copy Number Variant Discovery
Tools that analyze read coverage to detect copy number variants.
NameSummary
AnnotateIntervalsAnnotates intervals with GC content, mappability, and segmental-duplication content
CallCopyRatioSegmentsCalls copy-ratio segments as amplified, deleted, or copy-number neutral
CreateReadCountPanelOfNormalsCreates a panel of normals for read-count denoising
DenoiseReadCountsDenoises read counts to produce denoised copy ratios
DetermineGermlineContigPloidyDetermines the baseline contig ploidy for germline samples given counts data
FilterIntervalsFilters intervals based on annotations and/or count statistics
GermlineCNVCallerCalls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy
ModelSegmentsModels segmented copy ratios from denoised read counts and segmented minor-allele fractions from allelic counts
PlotDenoisedCopyRatiosCreates plots of denoised copy ratios
PlotModeledSegmentsCreates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates
PostprocessGermlineCNVCallsPostprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios
Coverage Analysis
Tools that count coverage, e.g. depth per allele
NameSummary
ASEReadCounterGenerates table of filtered base counts at het sites for allele specific expression
AnalyzeSaturationMutagenesis**BETA** (EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutagenesis experiment.
CollectAllelicCountsCollects reference and alternate allele counts at specified sites
CollectReadCountsCollects read counts at specified intervals
CountBasesCount bases in a SAM/BAM/CRAM file
CountBasesSparkCounts bases in the input SAM/BAM
CountReadsCount reads in a SAM/BAM/CRAM file
CountReadsSparkCounts reads in the input SAM/BAM
GetPileupSummariesTabulates pileup metrics for inferring contamination
PileupPrints 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
NameSummary
AccumulateVariantCallingMetrics (Picard)Combines multiple Variant Calling Metrics files into a single file
AnalyzeCovariatesEvaluate 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
CalculateContaminationCalculate the fraction of reads coming from cross-sample contamination
CalculateFingerprintMetrics (Picard)Calculate statistics on fingerprints, checking their viability
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
CheckPileupCompare 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.
CollectArraysVariantCallingMetrics (Picard)Collects summary and per-sample from the provided arrays VCF 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.
CollectSamErrorMetrics (Picard)Program to collect error metrics on bases stratified in various ways.
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.
CompareBaseQualitiesCompares 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
EstimateLibraryComplexity (Picard)Estimates the numbers of unique molecules in a sequencing library.
FlagStatAccumulate flag statistics given a BAM file
FlagStatSparkSpark tool to accumulate flag statistics
GetSampleNameEmit 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
NameSummary
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.
PreprocessIntervalsPrepares bins for coverage collection
SplitIntervalsSplit intervals into sub-interval files.
Metagenomics
Tools that perform metagenomic analysis, e.g. microbial community composition and pathogen detection
NameSummary
PathSeqBuildKmersBuilds set of host reference k-mers
PathSeqBuildReferenceTaxonomyBuilds a taxonomy datafile of the microbe reference
PathSeqBwaSparkStep 2: Aligns reads to the microbe reference
PathSeqFilterSparkStep 1: Filters low quality, low complexity, duplicate, and host reads
PathSeqPipelineSparkCombined tool that performs all steps: read filtering, microbe reference alignment, and abundance scoring
PathSeqScoreSparkStep 3: Classifies pathogen-aligned reads and generates abundance scores
Other
Miscellaneous tools, e.g. those that aid in data streaming
NameSummary
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
GatherBQSRReportsGathers scattered BQSR recalibration reports into a single file
GatherTranches**BETA** Gathers scattered VQSLOD tranches into a single file
IndexFeatureFileCreates 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**BETA** Condenses homRef blocks in a single-sample GVCF
Read Data Manipulation
Tools that manipulate read data in SAM, BAM or CRAM format
NameSummary
AddCommentsToBam (Picard)Adds comments to the header of a BAM file.
AddOATag (Picard)Record current alignment information to OA tag.
AddOrReplaceReadGroups (Picard)Assigns all the reads in a file to a single new read-group.
ApplyBQSRApply 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
BaseRecalibratorGenerates 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
ClipReadsClip 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.
FixMisencodedBaseQualityReadsFix Illumina base quality scores in a SAM/BAM/CRAM file
GatherBamFiles (Picard)Concatenate efficiently BAM files that resulted from a scattered parallel analysis
LeftAlignIndelsLeft-aligns indels from reads in a SAM/BAM/CRAM file
MarkDuplicates (Picard)Identifies duplicate reads.
MarkDuplicatesSparkMarkDuplicates 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.
PrintReadsPrint reads in the SAM/BAM/CRAM file
PrintReadsHeaderPrint the header from a SAM/BAM/CRAM file
PrintReadsSparkPrintReads 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.
RevertBaseQualityScoresRevert 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.
RevertSamSpark**BETA** 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)
SplitNCigarReadsSplit Reads with N in Cigar
SplitReadsOutputs 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.
UnmarkDuplicatesClears the 0x400 duplicate SAM flag
Reference
Tools that analyze and manipulate FASTA format references
NameSummary
BaitDesigner (Picard)Designs oligonucleotide baits for hybrid selection reactions.
BwaMemIndexImageCreatorCreate a BWA-MEM index image file for use with GATK BWA tools
CountBasesInReferenceCount the numbers of each base in a reference file
CreateSequenceDictionary (Picard)Creates a sequence dictionary for a reference sequence.
ExtractSequences (Picard)Subsets intervals from a reference sequence to a new FASTA file.
FastaAlternateReferenceMakerCreate an alternative reference by combining a fasta with a vcf.
FastaReferenceMakerCreate snippets of a 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)
NameSummary
CombineGVCFsMerges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations
GenomicsDBImportImport VCFs to GenomicsDB
GenotypeGVCFsPerform joint genotyping on one or more samples pre-called with HaplotypeCaller
GnarlyGenotyper**BETA** Perform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller
HaplotypeCallerCall germline SNPs and indels via local re-assembly of haplotypes
HaplotypeCallerSpark**BETA** HaplotypeCaller on Spark
Mutect2Call somatic SNVs and indels via local assembly of haplotypes
ReadsPipelineSpark**BETA** Runs BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller on unaligned or aligned reads to generate a VCF.
Structural Variant Discovery
Tools that detect structural variants
NameSummary
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
NameSummary
AnnotatePairOrientation**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
CalculateGenotypePosteriorsCalculate 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
CountVariantsCounts variant records in a VCF file, regardless of filter status.
CountVariantsSparkCountVariants 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
FuncotateSegments**BETA** Functional annotation for segment files. The output formats are not well-defined and subject to change.
FuncotatorFunctional Annotator
FuncotatorDataSourceDownloaderData source downloader for Funcotator.
GenotypeConcordance (Picard)Calculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.
ValidateBasicSomaticShortMutations**EXPERIMENTAL** Check variants against tumor-normal bams representing the same samples, though not the ones from the actual calls.
ValidateVariantsValidate VCF
VariantEval**BETA** General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
VariantsToTableExtract fields from a VCF file to a tab-delimited table
Variant Filtering
Tools that filter variants by annotating the FILTER column
NameSummary
ApplyVQSRApply a score cutoff to filter variants based on a recalibration table
CNNScoreVariantsApply 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
FilterMutectCallsFilter somatic SNVs and indels called by Mutect2
FilterVariantTranchesApply tranche filtering
FilterVcf (Picard)Hard filters a VCF.
VariantFiltrationFilter variant calls based on INFO and/or FORMAT annotations
VariantRecalibratorBuild a recalibration model to score variant quality for filtering purposes
Variant Manipulation
Tools that manipulate variant call format (VCF) data
NameSummary
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
LeftAlignAndTrimVariantsLeft 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
PrintVariantsSparkPrints 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.
SelectVariantsSelect 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.
UpdateVCFSequenceDictionaryUpdates 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 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
Base Calling
Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters
NameSummary
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.
Genotyping Arrays Manipulation
Tools that manipulate data generated by Genotyping arrays
NameSummary
CreateVerifyIDIntensityContaminationMetricsFile (Picard)Program to generate a picard metrics file from the output of the VerifyIDIntensity tool.
GtcToVcf (Picard)Program to convert a GTC file to a VCF
MergePedIntoVcf (Picard)Program to merge a single-sample ped file from zCall into a single-sample VCF.
VcfToAdpc (Picard)Program to convert an Arrays VCF to an ADPC file.
Methylation-Specific Tools
Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM
NameSummary
MethylationTypeCaller**EXPERIMENTAL** Identify methylated bases from bisulfite sequenced, methylation-aware BAMs
tools
NameSummary
AlleleFrequencyStratify by eval RODs by the allele frequency of the alternate allele
Read Filters
Applied by engine to select reads for analysis
NameSummary
AlignmentAgreesWithHeaderReadFilterFilters out reads where the alignment does not match the contents of the header
AllowAllReadsReadFilterDo not filter out any read
AmbiguousBaseReadFilterFilters out reads that have greater than the threshold number of N bases
CigarContainsNoNOperatorFilter out reads with CIGAR containing N operator
FirstOfPairReadFilterKeep only reads that are first of pair
FragmentLengthReadFilterKeep only read pairs with insert length less than or equal to the given value
GoodCigarReadFilterKeep only reads containing good CIGAR string
HasReadGroupReadFilterFilter out reads without Read Group
IntervalOverlapReadFilterFilters out reads that don't overlap the specified region. NOTE: This approach to extracting overlapping reads is very slow compared to using PrintReads and -L on an indexed bam file.
LibraryReadFilterKeep only reads from the specified library
MappedReadFilterFilter out unmapped reads
MappingQualityAvailableReadFilterFilter out reads without available mapping quality
MappingQualityNotZeroReadFilterFilter out reads with mapping quality equal to zero
MappingQualityReadFilterKeep only reads with mapping qualities within a specified range
MatchingBasesAndQualsReadFilterFilter out reads where the bases and qualities do not match
MateDifferentStrandReadFilterKeep only reads with mates mapped on the different strand
MateOnSameContigOrNoMappedMateReadFilterKeep only reads whose mate maps to the same contig or is unmapped
MateUnmappedAndUnmappedReadFilterFilters reads whose mate is unmapped as well as unmapped reads.
MetricsReadFilterFilter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments
NonChimericOriginalAlignmentReadFilterFilters reads whose original alignment was chimeric.
NonZeroFragmentLengthReadFilterFilter out reads with fragment length different from zero
NonZeroReferenceLengthAlignmentReadFilterFilter out reads that do not align to the reference
NotDuplicateReadFilterFilter out reads marked as duplicate
NotSecondaryAlignmentReadFilterFilter out reads representing secondary alignments
NotSupplementaryAlignmentReadFilterFilter out reads representing supplementary alignments
OverclippedReadFilterFilter out reads that are over-soft-clipped
PairedReadFilterFilter out unpaired reads
PassesVendorQualityCheckReadFilterFilter out reads failing platfor/vendor quality checks
PlatformReadFilterKeep only reads with matching Read Group platform
PlatformUnitReadFilterFilter out reads with matching platform unit attribute
PrimaryLineReadFilterKeep 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).
ProperlyPairedReadFilterKeep only reads that are properly paired
ReadGroupBlackListReadFilterKeep records not matching the read group tag and exact match string.
ReadGroupReadFilterKeep only reads from the specified read group
ReadLengthEqualsCigarLengthReadFilterFilter out reads where the read and CIGAR do not match in length
ReadLengthReadFilterKeep only reads whose length is within a certain range
ReadNameReadFilterKeep only reads with this read name
ReadStrandFilterKeep only reads whose strand is as specified
SampleReadFilterKeep only reads for a given sample
SecondOfPairReadFilterKeep only paired reads that are second of pair
SeqIsStoredReadFilterKeep only reads with sequenced bases
SoftClippedReadFilterFilter out reads that are over-soft-clipped
ValidAlignmentEndReadFilterKeep only reads where the read end is properly aligned
ValidAlignmentStartReadFilterKeep only reads with a valid alignment start
WellformedReadFilterKeep 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
NameSummary
AS_BaseQualityRankSumTestAllele-specific rank sum test of REF versus ALT base quality scores (AS_BaseQRankSum)
AS_FisherStrandAllele-specific strand bias estimated using Fisher's exact test (AS_FS)
AS_InbreedingCoeffAllele-specific likelihood-based test for the consanguinity among samples (AS_InbreedingCoeff)
AS_MappingQualityRankSumTestAllele-specific rank sum test for mapping qualities of REF versus ALT reads (AS_MQRankSum)
AS_QualByDepthAllele-specific call confidence normalized by depth of sample reads supporting the allele (AS_QD)
AS_RMSMappingQualityAllele-specific root-mean-square of the mapping quality of reads across all samples (AS_MQ)
AS_ReadPosRankSumTestAllele-specific rank sum test for relative positioning of REF versus ALT allele within reads (AS_ReadPosRankSum)
AS_StrandOddsRatioAllele-specific strand bias estimated by the symmetric odds ratio test (AS_SOR)
AlleleFractionVariant allele fraction for a genotype
BaseQualityMedian base quality of bases supporting each allele (MBQ)
BaseQualityRankSumTestRank sum test of REF versus ALT base quality scores (BaseQRankSum)
ChromosomeCountsCounts and frequency of alleles in called genotypes (AC, AF, AN)
ClippingRankSumTestRank sum test for hard-clipped bases on REF versus ALT reads (ClippingRankSum)
CountNsNumber of Ns at the pileup
CoverageTotal depth of coverage per sample and over all samples (DP)
DepthPerAlleleBySampleDepth of coverage of each allele per sample (AD)
DepthPerSampleHCDepth of informative coverage for each sample (DP)
ExcessHetPhred-scaled p-value for exact test of excess heterozygosity (ExcessHet)
FisherStrandStrand bias estimated using Fisher's exact test (FS)
FragmentLengthMedian fragment length of reads supporting each allele (MFRL)
GenotypeSummariesSummary of genotype statistics from all samples (NCC, GQ_MEAN, GQ_STDDEV)
InbreedingCoeffLikelihood-based test for the consanguinity among samples (InbreedingCoeff)
LikelihoodRankSumTestRank sum test of per-read likelihoods of REF versus ALT reads (LikelihoodRankSum)
MappingQualityMedian mapping quality of reads supporting each allele (MMQ)
MappingQualityRankSumTestRank sum test for mapping qualities of REF versus ALT reads (MQRankSum)
MappingQualityZeroCount of all reads with MAPQ = 0 across all samples (MQ0)
OrientationBiasReadCountsCount of read pairs in the F1R2 and F2R1 configurations supporting REF and ALT alleles (F1R2, F2R1)
OriginalAlignmentNumber of alt reads with an OA tag that doesn't match the current alignment contig.
PossibleDeNovoExistence of a de novo mutation in at least one of the given families (hiConfDeNovo, loConfDeNovo)
QualByDepthVariant confidence normalized by unfiltered depth of variant samples (QD)
RMSMappingQualityRoot mean square of the mapping quality of reads across all samples (MQ)
ReadPosRankSumTestRank sum test for relative positioning of REF versus ALT alleles within reads (ReadPosRankSum)
ReadPositionMedian distance of variant starts from ends of reads supporting each allele (MPOS)
ReferenceBasesAnnotate with local reference bases (REF_BASES)
SampleListList of samples that are not homozygous reference at a variant site (Samples)
StrandBiasBySampleNumber of forward and reverse reads that support REF and ALT alleles (SB)
StrandOddsRatioStrand bias estimated by the symmetric odds ratio test (SOR)
TandemRepeatTandem repeat unit composition and counts per allele (STR, RU, RPA)
UniqueAltReadCountNumber of non-duplicate-insert ALT reads (UNIQ_ALT_READ_COUNT)
网友评论