4.0.1.0
Tool documentation for GATK release 4.0.1.0
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IlluminaBasecallsToSam (Picard)
Transforms raw Illumina sequencing data into an unmapped SAM or BAM fil... -
InbreedingCoeff
Likelihood-based test for the consanguinity among samples (InbreedingCo... -
IndexFeatureFile
Creates an index for a feature file, e.g. VCF or BED file. Category... -
IntervalListToBed (Picard)
Converts an Picard IntervalList file to a BED file. Category I... -
IntervalListTools (Picard)
A tool for performing various IntervalList manipulations SummaryThis to... -
IntervalOverlapReadFilter
Filters out reads that don't overlap the specified region. NOTE: This a... -
LeftAlignAndTrimVariants
Left align and trim vairants Category Variant Manipulation ... -
LeftAlignIndels
Left-aligns indels from reads in a SAM/BAM/CRAM file Category ... -
LibraryReadFilter
Keep only reads from the specified library Category Read Filte... -
LiftOverIntervalList (Picard)
Lifts over an interval list from one reference build to another. This t... -
LiftoverVcf (Picard)
Lifts over a VCF file from one reference build to another. Summary Too... -
LikelihoodRankSumTest
Rank sum test of per-read likelihoods of REF versus ALT reads (Likeliho... -
MakeSitesOnlyVcf (Picard)
This tool reads a VCF/VCF.gz/BCF and removes all genotype information f... -
MappedReadFilter
Filter out unmapped reads Category Read Filters Overv... -
MappingQuality
Median mapping quality of reads supporting each allele (MMQ) Catego... -
MappingQualityAvailableReadFilter
Filter out reads without available mapping quality Category Re... -
MappingQualityNotZeroReadFilter
Filter out reads with mapping quality equal to zero Category R... -
MappingQualityRankSumTest
Rank sum test for mapping qualities of REF versus ALT reads (MQRankSum)... -
MappingQualityReadFilter
Keep only reads with mapping qualities within a specified range Cat... -
MappingQualityZero
Count of all reads with MAPQ = 0 across all samples (MQ0) Category ... -
MarkDuplicates (Picard)
Identifies duplicate reads. This tool locates and tags duplicate reads... -
MarkDuplicatesGATK (EXPERIMENTAL)
Examines aligned records in the supplied SAM/BAM/CRAM file to locate du... -
MarkDuplicatesSpark (BETA)
MarkDuplicates on Spark Category Read Data Manipulation ... -
MarkDuplicatesWithMateCigar (Picard)
Identifies duplicate reads, accounting for mate CIGAR. This tool locat... -
MarkIlluminaAdapters (Picard)
Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.... -
MatchingBasesAndQualsReadFilter
Filter out reads where the bases and qualities do not match Categor... -
MateDifferentStrandReadFilter
Keep only reads with mates mapped on the different strand Category ... -
MateOnSameContigOrNoMappedMateReadFilter
Keep only reads whose mate maps to the same contig or is unmapped C... -
MateUnmappedAndUnmappedReadFilter
Filters reads whose mate is unmapped as well as unmapped reads. Cat... -
MeanQualityByCycle (Picard)
Collect mean quality by cycle.This tool generates a data table and char...