终于讲完了Journal club，可以踏实下来继续学习生信知识啦~
这篇学习笔记主要是对GATK有一个初步了解，就是要先知道它是干嘛的。GATK这个软件的功能太多太多了。。。看了官网以后感觉无从下手，从来没有接触过GATK的我这么多东西可咋学？参考大神的文章：GATK入门的最佳姿势，别犹豫，直接上，就对了。
先来看看GATK的官网吧：https://gatk.broadinstitute.org/hc/en-us
GATK的英文全称是genome analysis toolkit（基因组分析工具）。根据官网的介绍，这个软件主要是用来发现突变体（variant）。
GATK是鉴定germline DNA和RNAseq数据中的SNPs和indels的"工业标准"。它的使用范围正在逐渐的扩大，包括体细胞短变异体calling、处理拷贝数(CNV)和结构变异(SV)。除了突变体caller之外，GATK还包括许多功能来执行相关任务，比如对高通量测序的数据处理和质量控制，并绑定了时下非常流行的Picard。
这些工具主要用于处理由Illumina测序技术生成的外显体和全基因组，但它们也可以用于处理各种其他技术和实验设计。尽管GATK最初是为人类基因组学而开发的，但它目前已经进化到可以处理任何多倍体生物的基因组数据。
现在GATK最新版是4.1.8.1，你在官网上可以查阅所有版本的参数说明：here，可以说是非常的详细了。
GATK需要在Linux和其他posix兼容的平台上运行，其中包括MacOS x。Windows系统不受支持GATK。主要的系统需求是Java 8 / JDK 1.8。其中有一些工具需要依赖R或Python。你可以在这个网站：Download了解下载和安装说明。具体下载方法就不赘述了，因为像这种数据一般也只能在服务器上运行，由于我们学校的服务器里已经安装好了GATK，所以就直接拿来调用就可以了~
简单的看一下GATK都有哪些tool，在命令行里输入：
$ gatk --list
这时会弹出一大串信息，每一个功能都用虚线隔开了，并且在每一个参数后面都有介绍是什么用途：
Using GATK jar /gpfs/share/apps/gatk/4.1.7.0/gatk-package-4.1.7.0-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=2 -jar /gpfs/share/apps/gatk/4.1.7.0/gatk-package-4.1.7.0-local.jar --help
USAGE: [-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 Annotates intervals with GC content, mappability, and segmental-duplication content
CallCopyRatioSegments 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 Creates a panel of normals for read-count denoising
DenoiseReadCounts Denoises read counts to produce denoised copy ratios
DetermineGermlineContigPloidy Determines the baseline contig ploidy for germline samples given counts data
FilterIntervals Filters intervals based on annotations and/or count statistics
GermlineCNVCaller Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy
MergeAnnotatedRegions (EXPERIMENTAL Tool) Merge annotated genomic regions based entirely on touching/overlapping intervals.
MergeAnnotatedRegionsByAnnotation (EXPERIMENTAL Tool) Merge annotated genomic regions within specified distance if annotation value(s) are exactly the same.
ModelSegments Models segmented copy ratios from denoised read counts and segmented minor-allele fractions from allelic counts
PlotDenoisedCopyRatios Creates plots of denoised copy ratios
PlotModeledSegments Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates
PostprocessGermlineCNVCalls Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios
TagGermlineEvents (EXPERIMENTAL Tool) Do a simplistic tagging of germline events in a tumor segment file.
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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
AnalyzeSaturationMutagenesis (BETA Tool) (EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutagenesis experiment.
CollectAllelicCounts Collects reference and alternate allele counts at specified sites
CollectAllelicCountsSpark Collects reference and alternate allele counts at specified sites
CollectF1R2Counts Collect F1R2 read counts for the Mutect2 orientation bias mixture model filter
CollectReadCounts Collects read counts at specified intervals
CountBases Count bases in a SAM/BAM/CRAM file
CountBasesSpark Counts bases in the input SAM/BAM
CountReads Count reads in a SAM/BAM/CRAM file
CountReadsSpark Counts reads in the input SAM/BAM
DepthOfCoverage (BETA Tool) Generate coverage summary information for reads data
GetPileupSummaries 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
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
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.
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 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) (EXPERIMENTAL Tool) Estimates the rate of independent replication rate 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.
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 Tool) 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.
EstimateLibraryComplexity (Picard) Estimates the numbers of unique molecules in a sequencing library.
FlagStat Accumulate flag statistics given a BAM file
FlagStatSpark Spark tool to accumulate flag statistics
GatherPileupSummaries Combine output files from GetPileupSummary in the order defined by a sequence dictionary
GetSampleName 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
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Genotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays
CombineGenotypingArrayVcfs (Picard) Program to combine multiple genotyping array VCF files into one VCF.
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.
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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.
CompareIntervalLists Compare two interval lists for equality
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 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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Methylation-Specific Tools: Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM
MethylationTypeCaller (EXPERIMENTAL Tool) Identify methylated bases from bisulfite sequenced, methylation-aware BAMs
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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
PrintBGZFBlockInformation (EXPERIMENTAL Tool) Print information about the compressed blocks in a BGZF format file
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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.
AddOATag (Picard) Record current alignment information to OA tag.
AddOrReplaceReadGroups (Picard) Assigns all the reads in a file to a single new read-group.
AddOriginalAlignmentTags (EXPERIMENTAL Tool) Adds Original Alignment tag and original mate contig tag
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
BuildBamIndex (Picard) Generates a BAM index ".bai" file.
BwaAndMarkDuplicatesPipelineSpark (BETA Tool) Takes name-sorted file and runs BWA and MarkDuplicates.
BwaSpark (BETA Tool) Align reads to a given reference using BWA on Spark
CleanSam (Picard) Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
ClipReads Clip reads in a SAM/BAM/CRAM file
CollectDuplicateMetrics (Picard) Collect Duplicate metrics from marked file.
ConvertHeaderlessHadoopBamShardToBam (BETA Tool) Convert a headerless BAM shard into a readable BAM
DownsampleByDuplicateSet (BETA Tool) Discard a set fraction of duplicate sets from a UMI-grouped 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.
MarkDuplicatesSpark 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
PrintReadsHeader Print the header from a SAM/BAM/CRAM file
PrintReadsSpark 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.
RevertSamSpark (BETA Tool) 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) (EXPERIMENTAL Tool) 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) (EXPERIMENTAL 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
CountBasesInReference Count 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.
FastaAlternateReferenceMaker Create an alternative reference by combining a fasta with a vcf.
FastaReferenceMaker Create snippets of a 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
GnarlyGenotyper (BETA Tool) Perform "quick and dirty" 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
LearnReadOrientationModel Get the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter
MergeMutectStats Merge the stats output by scatters of a single Mutect2 job
Mutect2 Call somatic SNVs and indels via local assembly of haplotypes
ReadsPipelineSpark (BETA Tool) Runs BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller on unaligned or aligned reads to generate a VCF.
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Structural Variant Discovery: Tools that detect structural variants
CpxVariantReInterpreterSpark (BETA Tool) (Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf
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
PairedEndAndSplitReadEvidenceCollection (BETA Tool) Gathers paired-end and split read evidence files for use in the GATK-SV pipeline.
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
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Variant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine
AlleleFrequencyQC (BETA Tool) General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
AnnotateVcfWithBamDepth (Internal) Annotate a vcf with a bam's read depth at each variant locus
AnnotateVcfWithExpectedAlleleFraction (Internal) Annotate a vcf with expected allele fractions in pooled sequencing
CalculateGenotypePosteriors Calculate genotype posterior probabilities given family and/or known population genotypes
CalculateMixingFractions (Internal) Calculate proportions of different samples in a pooled bam
Concordance 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 CountVariants on Spark
EvaluateInfoFieldConcordance (BETA Tool) Evaluate concordance of info fields in an input VCF against a validated truth VCF
FilterFuncotations (EXPERIMENTAL Tool) Filter variants based on clinically-significant Funcotations.
FindMendelianViolations (Picard) Finds mendelian violations of all types within a VCF
FuncotateSegments (BETA Tool) Functional annotation for segment files. The output formats are not well-defined and subject to change.
Funcotator Functional Annotator
FuncotatorDataSourceDownloader Data 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.
MergeMutect2CallsWithMC3 (EXPERIMENTAL Tool) UNSUPPORTED. FOR EVALUATION ONLY. Merge M2 calls with MC
ValidateBasicSomaticShortMutations (EXPERIMENTAL Tool) Check variants against tumor-normal bams representing the same samples, though not the ones from the actual calls.
ValidateVariants Validate VCF
VariantEval (BETA Tool) General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
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
CNNScoreVariants 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
CreateSomaticPanelOfNormals (BETA Tool) Make a panel of normals for use with Mutect2
FilterAlignmentArtifacts (EXPERIMENTAL Tool) Filter alignment artifacts from a vcf callset.
FilterMutectCalls Filter somatic SNVs and indels called by Mutect2
FilterVariantTranches Apply tranche filtering
FilterVcf (Picard) Hard filters a VCF.
MTLowHeteroplasmyFilterTool If too many low het sites, filter all low het sites
NuMTFilterTool Uses the median autosomal coverage and the allele depth to determine whether the allele might be a NuMT
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
LeftAlignAndTrimVariants Left align and trim vairants
LiftoverVcf (Picard) Lifts over a VCF file from one reference build to another.
MakeSitesOnlyVcf (Picard) Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
MakeVcfSampleNameMap (Picard) Creates a TSV from sample name to VCF/GVCF path, with one line per input.
MergeVcfs (Picard) Combines multiple variant files into a single variant file
PrintVariantsSpark 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 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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可以看出来这个软件太强大了。这里有一篇非常好，非常详细的文章，可以让GATK小白们对GATK的分析流程有一个大体的了解：从零开始完整学习全基因组测序（WGS）数据分析：第4节 构建WGS主流程。
在之后的笔记里会记录对GATK的后续学习。