4.0.5.2
Tool documentation for GATK release 4.0.5.2
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PlotDenoisedCopyRatios (BETA)
Creates plots of denoised copy ratios Category Copy Nu... -
PlotModeledSegments (BETA)
Creates plots of denoised and segmented copy-ratio and minor-al... -
PolymorphicNuMT
Number of alts indicates it could be an autosomal false positiv... -
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 (BETA)
Postprocesses the output of GermlineCNVCaller and generates VCF... -
PreprocessIntervals (BETA)
Prepares bins for coverage collection Category Interva... -
PrimaryLineReadFilter
Keep only reads representing primary alignments (those that sat... -
PrintReads
Print reads in the SAM/BAM/CRAM file Category Read Dat... -
PrintReadsSpark (BETA)
PrintReads on Spark Category Read Data Manipulation ... -
PrintVariantsSpark (BETA)
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... -
ReadGroupBlackListReadFilter
Keep records not matching the read group tag and exact match st... -
ReadGroupReadFilter
Keep only reads from the specified read group Category ... -
ReadLengthEqualsCigarLengthReadFilter
Filter out reads where the read and CIGAR do not match in leng... -
ReadLengthReadFilter
Keep only reads whose length is within a certain range Cate... -
ReadNameReadFilter
Keep only reads with this read name Category Read Filt... -
ReadPosition
Median distance of variant starts from ends of reads supporting... -
ReadPosRankSumTest
Rank sum test for relative positioning of REF versus ALT allele... -
ReadsPipelineSpark (BETA)
Takes unaligned or aligned reads and runs BWA (if specified), M... -
ReadStrandFilter
Keep only reads whose strand is as specified Category ... -
ReblockGVCF (EXPERIMENTAL)
Condenses homRef blocks in a single-sample GVCF Category ... -
ReferenceBases
Annotate with local reference bases (REF_BASES) Category ... -
RemoveNearbyIndels
(Internal) Remove indels from the VCF file that are close to ea... -
RenameSampleInVcf (Picard)
This tool enables the user to rename a sample in either a VCF o... -
ReorderSam (Picard)
Not to be confused with SortSam which sorts a SAM or BAM file w... -
ReplaceSamHeader (Picard)
Replaces the SAMFileHeader in a SAM or BAM file. This tool mak...