4.0.6.0
Tool documentation for GATK release 4.0.6.0
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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 (UNIQ_ALT_READ_COUNT) ... -
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 the variants in a VCF against a tumor-normal pair of bams... -
ValidateSamFile (Picard)
Validates a SAM or BAM file.This tool reports on the validity o... -
ValidateVariants
Validate VCF Category Variant Evaluation and Refinemen... -
VariantAnnotator (BETA)
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... -
VcfToAdpc (Picard)
VcfToAdpc takes a VCF, as generated by GtcToVcf and generates a... -
VcfToIntervalList (Picard)
This tool creates a Picard Interval List from a VCF or BCF. It ... -
ViewSam (Picard)
Very simple command that just reads a SAM or BAM file andwrites... -
WellformedReadFilter
Keep only reads that are well-formed Category Read Fil...