4.0.5.0
Tool documentation for GATK release 4.0.5.0
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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 or BAM files to a previous state. Category ... -
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... -
SimpleMarkDuplicatesWithMateCigar (Picard) (BETA)
Examines aligned records in the supplied SAM or BAM file to loc... -
SoftClippedReadFilter
Filter out reads that are over-soft-clipped Category R... -
SortSam (Picard)
This tool sorts the input SAM or BAM file by coordinate, queryn... -
SortSamSpark (BETA)
SortSam on Spark (works on SAM/BAM/CRAM) Category Read... -
SortVcf (Picard)
Sorts one or more VCF files. This tool sorts the records in VC... -
SplitIntervals
Split intervals into sub-interval files. Category Inte... -
SplitNCigarReads
Split Reads with N in Cigar Category Read Data Manipul... -
SplitReads
Outputs reads from a SAM/BAM/CRAM by read group, sample and lib... -
SplitSamByLibrary (Picard)
Takes a SAM or BAM file and separates all the reads into one SA... -
SplitSamByNumberOfReads (Picard)
Splits a SAM or BAM file to multiple BAMs.This tool splits the ... -
SplitVcfs (Picard)
Splits SNPs and INDELs into separate files. This tool reads in... -
StrandArtifact
Annotations for strand artifact filter (SA_POST_PROB, SA_MAP_AF... -
StrandBiasBySample
Number of forward and reverse reads that support REF and ALT al... -
StrandOddsRatio
Strand bias estimated by the symmetric odds ratio test (SOR) ... -
StructuralVariationDiscoveryPipelineSpark (BETA)
Runs the structural variation discovery workflow on a single sa...