4.0.1.0
Tool documentation for GATK release 4.0.1.0
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PileupSpark (BETA)
Prints read alignments in samtools pileup format Category Cove... -
PlatformReadFilter
Keep only reads with matching Read Group platform Category Rea... -
PlatformUnitReadFilter
Filter out reads with matching platform unit attribute Category ... -
PlotDenoisedCopyRatios (BETA)
Creates plots of denoised copy ratios Category Copy Number Var... -
PlotModeledSegments (BETA)
Creates plots of denoised and segmented copy-ratio and minor-allele-fra... -
PolymorphicNuMT
Number of alts indicates it could be an autosomal false positive. C... -
PositionBasedDownsampleSam (Picard)
Summary Class to downsample a SAM/BAM file based on the position of the... -
PossibleDeNovo
Existence of a de novo mutation in at least one of the given families (... -
PostprocessGermlineCNVCalls (BETA)
Postprocesses the output of GermlineCNVCaller and generates VCF files. ... -
PreprocessIntervals (BETA)
Prepares bins for coverage collection Category Intervals Manip... -
PrimaryLineReadFilter
Keep only reads representing primary alignments (those that satisfy bot... -
PrintReads
Print reads in the SAM/BAM/CRAM file Category Read Data Manipu... -
PrintReadsSpark (BETA)
PrintReads on Spark Category Read Data Manipulation O... -
PrintVariantsSpark (BETA)
Prints out variants from the input VCF. Category Variant Manip... -
ProperlyPairedReadFilter
Keep only reads that are properly paired Category Read Filters... -
QualByDepth
Variant confidence normalized by unfiltered depth of variant samples (Q... -
QualityScoreDistribution (Picard)
Chart the distribution of quality scores. This tool is used for determ... -
QualityScoreDistributionSpark (BETA)
QualityScoreDistribution on Spark Category Diagnostics and Qua... -
ReadGroupBlackListReadFilter
Keep records not matching the read group tag and exact match string. ... -
ReadGroupReadFilter
Keep only reads from the specified read group Category Read Fi... -
ReadLengthEqualsCigarLengthReadFilter
Filter out reads where the read and CIGAR do not match in length C... -
ReadLengthReadFilter
Keep only reads whose length is within a certain range Category ... -
ReadNameReadFilter
Keep only reads with this read name Category Read Filters ... -
ReadPosition
Median distance of variant starts from ends of reads supporting each al... -
ReadPosRankSumTest
Rank sum test for relative positioning of REF versus ALT alleles within... -
ReadsPipelineSpark (BETA)
Takes unaligned or aligned reads and runs BWA (if specified), MarkDupli... -
ReadStrandFilter
Keep only reads whose strand is as specified Category Read Fil... -
ReblockGVCF (EXPERIMENTAL)
Condenses homRef blocks in a single-sample GVCF Category Other... -
ReferenceBases
Annotate with local reference bases (REF_BASES) Category Varia... -
RemoveNearbyIndels
(Internal) Remove indels from the VCF file that are close to each other...