4.2.3.0
Tool documentation for GATK release 4.2.3.0
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SortSam (Picard)
This tool sorts the input SAM or BAM file by coordinate, queryn... -
SortSamSpark (BETA)
SortSam on Spark (works on SAM/BAM/CRAM) Category Read... -
SortVcf (Picard)
Sorts one or more VCF files. This tool sorts the records in VC... -
SplitIntervals
Split intervals into sub-interval files. Category Inte... -
SplitNCigarReads
Split Reads with N in Cigar Category Read Data Manipul... -
SplitReads
Outputs reads from a SAM/BAM/CRAM by read group, sample and lib... -
SplitSamByLibrary (Picard)
Takes a SAM or BAM file and separates all the reads into one SA... -
SplitSamByNumberOfReads (Picard)
Splits a SAM or BAM file to multiple BAMs.This tool splits the ... -
SplitVcfs (Picard)
Splits SNPs and INDELs into separate files. This tool reads in... -
StrandBiasBySample
Number of forward and reverse reads that support REF and ALT al... -
StrandOddsRatio
Strand bias estimated by the symmetric odds ratio test (SOR) ... -
StructuralVariationDiscoveryPipelineSpark (BETA)
Runs the structural variation discovery workflow on a single sa... -
SvDiscoverFromLocalAssemblyContigAlignmentsSpark (BETA)
(Internal) Examines aligned contigs from local assemblies and c... -
TandemRepeat
Tandem repeat unit composition and counts per allele (STR, RU, ... -
UmiAwareMarkDuplicatesWithMateCigar (Picard) (EXPERIMENTAL)
Identifies duplicate reads using information from read position... -
UniqueAltReadCount
Number of non-duplicate-insert ALT reads (AS_UNIQ_ALT_READ_COUN... -
UnmarkDuplicates
Clears the 0x400 duplicate SAM flag Category Read Data... -
UpdateVCFSequenceDictionary
Updates the sequence dictionary in a variant file. Category... -
UpdateVcfSequenceDictionary (Picard)
Takes a VCF and a second file that contains a sequence dictiona... -
ValidAlignmentEndReadFilter
Keep only reads where the read end is properly aligned Cate... -
ValidAlignmentStartReadFilter
Keep only reads with a valid alignment start Category ... -
ValidateBasicSomaticShortMutations (EXPERIMENTAL)
Check variants against tumor-normal bams representing the same ... -
ValidateSamFile (Picard)
Validates a SAM or BAM file.This tool reports on the validity o... -
ValidateVariants
Validate VCF Category Variant Evaluation and Refinemen... -
VariantAnnotator
Tool for adding annotations to VCF files Category Vari... -
VariantEval (BETA)
General-purpose tool for variant evaluation (% in dbSNP, genoty... -
VariantFiltration
Filter variant calls based on INFO and/or FORMAT annotations ... -
VariantRecalibrator
Build a recalibration model to score variant quality for filter... -
VariantsToTable
Extract fields from a VCF file to a tab-delimited table Cat... -
VcfFormatConverter (Picard)
Converts VCF to BCF or BCF to VCF. This tool converts files be...