4.2.3.0
Tool documentation for GATK release 4.2.3.0
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PathSeqBuildReferenceTaxonomy
Builds a taxonomy datafile of the microbe reference Categor... -
PathSeqBwaSpark
Step 2: Aligns reads to the microbe reference Category ... -
PathSeqFilterSpark
Step 1: Filters low quality, low complexity, duplicate, and hos... -
PathSeqPipelineSpark
Combined tool that performs all steps: read filtering, microbe ... -
PathSeqScoreSpark
Step 3: Classifies pathogen-aligned reads and generates abundan... -
Pileup
Prints read alignments in samtools pileup format Category ... -
PileupSpark (BETA)
Prints read alignments in samtools pileup format Category ... -
PlatformReadFilter
Keep only reads with matching Read Group platform Category ... -
PlatformUnitReadFilter
Filter out reads with matching platform unit attribute Cate... -
PlotDenoisedCopyRatios
Creates plots of denoised copy ratios Category Copy Nu... -
PlotModeledSegments
Creates plots of denoised and segmented copy-ratio and minor-al... -
PositionBasedDownsampleSam (Picard)
Summary Class to downsample a SAM/BAM file based on the positio... -
PossibleDeNovo
Existence of a de novo mutation in at least one of the given fa... -
PostprocessGermlineCNVCalls
Postprocesses the output of GermlineCNVCaller and generates VCF... -
PreprocessIntervals
Prepares bins for coverage collection Category Interva... -
PrimaryLineReadFilter
Keep only reads representing primary alignments (those that sat... -
PrintDistantMates
Unmaps reads with distant mates. Category Read Data Ma... -
PrintReads
Print reads in the SAM/BAM/CRAM file Category Read Dat... -
PrintReadsHeader
Print the header from a SAM/BAM/CRAM file Category Rea... -
PrintReadsSpark
PrintReads on Spark Category Read Data Manipulation ... -
PrintSVEvidence (EXPERIMENTAL)
Prints SV evidence records Category Structural Variant... -
PrintVariantsSpark
Prints out variants from the input VCF. Category Varia... -
ProperlyPairedReadFilter
Keep only reads that are properly paired Category Read... -
QualByDepth
Variant confidence normalized by unfiltered depth of variant sa... -
QualityScoreDistribution (Picard)
Chart the distribution of quality scores. This tool is used fo... -
QualityScoreDistributionSpark (BETA)
QualityScoreDistribution on Spark Category Diagnostics... -
ReadAnonymizer (EXPERIMENTAL)
Replace bases in reads with reference bases. Category ... -
ReadGroupBlackListReadFilter
Keep records that don't match the specified filter string(s). ... -
ReadGroupReadFilter
Keep only reads from the specified read group Category ... -
ReadLengthEqualsCigarLengthReadFilter
Filter out reads where the read and CIGAR do not match in leng...