Logo
User Guide Tool Index Blog Forum DRAGEN-GATK Events Download GATK4
Sign in

Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

  1. GATK
  2. Tool Index
  3. 4.0.2.0

4.0.2.0

Follow New articles New articles and comments

Tool documentation for GATK release 4.0.2.0

  • SplitVcfs (Picard)
    Splits SNPs and INDELs into separate files. This tool reads in a VCF o...
  • StrandArtifact
    Annotations for strand artifact filter (SA_POST_PROB, SA_MAP_AF) Ca...
  • StrandBiasBySample
    Number of forward and reverse reads that support REF and ALT alleles (S...
  • StrandOddsRatio
    Strand bias estimated by the symmetric odds ratio test (SOR) Catego...
  • StructuralVariationDiscoveryPipelineSpark (BETA)
    Runs the structural variation discovery workflow on a single sample ...
  • SvDiscoverFromLocalAssemblyContigAlignmentsSpark (BETA)
    (Internal) Examines aligned contigs from local assemblies and calls com...
  • SvDiscoverFromLocalAssemblyContigAlignmentsSpark (BETA)
    (Internal) Examines aligned contigs from local assemblies and calls com...
  • TandemRepeat
    Tandem repeat unit composition and counts per allele (STR, RU, RPA) ...
  • UmiAwareMarkDuplicatesWithMateCigar (Picard) (BETA)
    Identifies duplicate reads using information from read positions and UM...
  • UniqueAltReadCount
    Number of non-duplicate-insert ALT reads (UNIQ_ALT_READ_COUNT) Cate...
  • UnmarkDuplicates
    Clears the 0x400 duplicate SAM flag Category Read Data Manipul...
  • UpdateVCFSequenceDictionary
    Updates the sequence dictionary in a variant file. Category Va...
  • UpdateVcfSequenceDictionary (Picard)
    Takes a VCF and a second file that contains a sequence dictionary and u...
  • ValidAlignmentEndReadFilter
    Keep only reads where the read end is properly aligned Category ...
  • ValidAlignmentStartReadFilter
    Keep only reads with a valid alignment start Category Read Fil...
  • ValidateBasicSomaticShortMutations (EXPERIMENTAL)
    Check the variants in a VCF against a tumor-normal pair of bams represe...
  • ValidateSamFile (Picard)
    Validates a SAM or BAM file.This tool reports on the validity of a SAM ...
  • ValidateVariants
    Validate VCF Category Variant Evaluation and Refinement ...
  • VariantAnnotator (BETA)
    Tool for adding annotations to VCF files Category Variant Mani...
  • VariantEval (BETA)
    General-purpose tool for variant evaluation (% in dbSNP, genotype conco...
  • VariantFiltration
    Filter variant calls based on INFO and/or FORMAT annotations Catego...
  • VariantRecalibrator
    Build a recalibration model to score variant quality for filtering purp...
  • VariantsToTable
    Extract fields from a VCF file to a tab-delimited table Category ...
  • VcfFormatConverter (Picard)
    Converts VCF to BCF or BCF to VCF. This tool converts files between th...
  • VcfToAdpc (Picard)
    VcfToAdpc takes a VCF, as generated by GtcToVcf and generates an Illumi...
  • VcfToIntervalList (Picard)
    This tool creates a Picard Interval List from a VCF or BCF. It is impor...
  • ViewSam (Picard)
    Very simple command that just reads a SAM or BAM file andwrites out the...
  • WellformedReadFilter
    Keep only reads that are well-formed Category Read Filters ...
  • «
  • ‹
  • 6
  • 7
  • 8
  • 9
  • 10
  • 11

footer-logo © Broad Institute

  • twitter icon
  • facebook icon
  • linkedin icon
Powered by Zendesk