4.2.3.0
Tool documentation for GATK release 4.2.3.0
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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)
Runs BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCal... -
ReadStrandFilter
Keep only reads whose strand is as specified Category ... -
ReblockGVCF
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... -
RevertBaseQualityScores
Revert Quality Scores in a SAM/BAM/CRAM file Category ... -
RevertOriginalBaseQualitiesAndAddMateCigar (Picard)
Reverts the original base qualities and adds the mate cigar tag... -
RevertSam (Picard)
Reverts SAM or BAM files to a previous state. This tool remove... -
RevertSamSpark (BETA)
Reverts SAM, BAM or CRAM files to a previous state. Categor... -
RMSMappingQuality
Root mean square of the mapping quality of reads across all sam... -
SamFormatConverter (Picard)
Convert a BAM file to a SAM file, or SAM to BAM. Input and outp... -
SampleList
List of samples that are not homozygous reference at a variant ... -
SampleReadFilter
Keep only reads for a given sample Category Read Filte... -
SamToFastq (Picard)
Converts a SAM or BAM file to FASTQ. Extracts read sequences an... -
ScatterIntervalsByNs (Picard)
Writes an interval list created by splitting a reference at Ns.... -
SecondOfPairReadFilter
Keep only paired reads that are second of pair Category ... -
SelectVariants
Select a subset of variants from a VCF file Category V... -
SeqIsStoredReadFilter
Keep only reads with sequenced bases Category Read Fil... -
SetNmAndUqTags (Picard)
DEPRECATED: Use SetNmMdAndUqTags instead.This tool takes in a c... -
SetNmMdAndUqTags (Picard)
This tool takes in a coordinate-sorted SAM or BAM and calculate... -
ShiftFasta (BETA)
Creates a shifted fasta file and shift_back file Category ... -
SimpleMarkDuplicatesWithMateCigar (Picard) (EXPERIMENTAL)
Examines aligned records in the supplied SAM or BAM file to loc... -
SoftClippedReadFilter
Filter out reads that are over-soft-clipped Category R...