4.0.2.0
Tool documentation for GATK release 4.0.2.0
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RemoveNearbyIndels
(Internal) Remove indels from the VCF file that are close to each other... -
RenameSampleInVcf (Picard)
This tool enables the user to rename a sample in either a VCF or BCF fi... -
ReorderSam (Picard)
Not to be confused with SortSam which sorts a SAM or BAM file with a va... -
ReplaceSamHeader (Picard)
Replaces the SAMFileHeader in a SAM or BAM file. This tool makes it po... -
RevertBaseQualityScores
Revert Quality Scores in a SAM/BAM/CRAM file Category Read Dat... -
RevertOriginalBaseQualitiesAndAddMateCigar (Picard)
Reverts the original base qualities and adds the mate cigar tag to read... -
RevertSam (Picard)
Reverts SAM or BAM files to a previous state. This tool removes or res... -
RevertSamSpark (BETA)
Reverts SAM or BAM files to a previous state. Category Read Da... -
RMSMappingQuality
Root mean square of the mapping quality of reads across all samples (MQ... -
SamFormatConverter (Picard)
Convert a BAM file to a SAM file, or SAM to BAM. Input and output forma... -
SampleList
List of samples that are not homozygous reference at a variant site (Sa... -
SampleReadFilter
Keep only reads for a given sample Category Read Filters ... -
SamToFastq (Picard)
Converts a SAM or BAM file to FASTQ.Extracts read sequences and qualiti... -
ScatterIntervalsByNs (Picard)
Writes an interval list created by splitting a reference at Ns.A Progra... -
SecondOfPairReadFilter
Keep only paired reads that are second of pair Category Read F... -
SelectVariants
Select a subset of variants from a VCF file Category Variant M... -
SeqIsStoredReadFilter
Keep only reads with sequenced bases Category Read Filters ... -
SetNmAndUqTags (Picard)
DEPRECATED: Use SetNmMdAndUqTags instead.This tool takes in a coordinat... -
SetNmMdAndUqTags (Picard)
This tool takes in a coordinate-sorted SAM or BAM and calculatesthe NM,... -
SimpleMarkDuplicatesWithMateCigar (Picard) (BETA)
Examines aligned records in the supplied SAM or BAM file to locate dupl... -
SoftClippedReadFilter
Filter out reads that are over-soft-clipped Category Read Filt... -
SortReadFileSpark (BETA)
SortSam on Spark (works on SAM/BAM/CRAM) Category Read Data Ma... -
SortSam (Picard)
This tool sorts the input SAM or BAM file by coordinate, queryname (QNA... -
SortSamSpark (BETA)
SortSam on Spark (works on SAM/BAM/CRAM) Category Read Data Ma... -
SortVcf (Picard)
Sorts one or more VCF files. This tool sorts the records in VCF files ... -
SplitIntervals
Split intervals into sub-interval files. Category Intervals Ma... -
SplitNCigarReads
Split Reads with N in Cigar Category Read Data Manipulation ... -
SplitReads
Outputs reads from a SAM/BAM/CRAM by read group, sample and library nam... -
SplitSamByLibrary (Picard)
Takes a SAM or BAM file and separates all the reads into one SAM or BAM... -
SplitSamByNumberOfReads (Picard)
Splits a SAM or BAM file to multiple BAMs.This tool splits the input qu...