4.0.2.0
Tool documentation for GATK release 4.0.2.0
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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 ...