4.2.4.0
Tool documentation for GATK release 4.2.4.0
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HaplotypeCallerSpark (BETA)
HaplotypeCaller on Spark Category Short Variant Discov... -
HasReadGroupReadFilter
Filter out reads without Read Group Category Read Filt... -
IlluminaBasecallsToFastq (Picard)
Generate FASTQ file(s) from Illumina basecall read data. This ... -
IlluminaBasecallsToSam (Picard)
Transforms raw Illumina sequencing data into an unmapped SAM or... -
InbreedingCoeff
Likelihood-based test for the consanguinity among samples (Inbr... -
IndexFeatureFile
Creates an index for a feature file, e.g. VCF or BED file. ... -
IntervalListToBed (Picard)
Converts an Picard IntervalList file to a BED file. Categor... -
IntervalListTools (Picard)
A tool for performing various IntervalList manipulations Summar... -
IntervalOverlapReadFilter
Filters out reads that don't overlap the specified region. NOTE... -
LearnReadOrientationModel
Get the maximum likelihood estimates of artifact prior probabil... -
LeftAlignAndTrimVariants
Left align and trim vairants Category Variant Manipula... -
LeftAlignIndels
Left-aligns indels from reads in a SAM/BAM/CRAM file Catego... -
LibraryReadFilter
Keep only reads from the specified library Category Re... -
LiftOverIntervalList (Picard)
Lifts over an interval list from one reference build to another... -
LiftoverVcf (Picard)
Lifts over a VCF file from one reference build to another. Sum... -
LikelihoodRankSumTest
Rank sum test of per-read likelihoods of REF versus ALT reads (... -
LocalAssembler (BETA)
Local assembler for SVs Category Coverage Analysis ... -
MakeSitesOnlyVcf (Picard)
This tool reads a VCF/VCF.gz/BCF and removes all genotype infor... -
MappedReadFilter
Filter out unmapped reads Category Read Filters ... -
MappingQuality
Median mapping quality of reads supporting each allele (MMQ) ... -
MappingQualityAvailableReadFilter
Filter out reads without available mapping quality Category... -
MappingQualityNotZeroReadFilter
Filter out reads with mapping quality equal to zero Categor... -
MappingQualityRankSumTest
Rank sum test for mapping qualities of REF versus ALT reads (MQ... -
MappingQualityReadFilter
Keep only reads with mapping qualities within a specified range... -
MappingQualityZero
Count of all reads with MAPQ = 0 across all samples (MQ0) C... -
MarkDuplicates (Picard)
Identifies duplicate reads. This tool locates and tags duplica... -
MarkDuplicatesSpark
MarkDuplicates on Spark Category Read Data Manipulatio... -
MarkDuplicatesWithMateCigar (Picard)
Identifies duplicate reads, accounting for mate CIGAR. This to... -
MarkIlluminaAdapters (Picard)
Reads a SAM or BAM file and rewrites it with new adapter-trimmi... -
MatchingBasesAndQualsReadFilter
Filter out reads where the bases and qualities do not match ...