4.2.3.0
Tool documentation for GATK release 4.2.3.0
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BamToBfq (Picard)
Converts a BAM file into a BFQ (binary fastq formatted) file.Th... -
BaseQuality
Median base quality of bases supporting each allele (MBQ) C... -
BaseQualityRankSumTest
Rank sum test of REF versus ALT base quality scores (BaseQRankS... -
BaseRecalibrator
Generates recalibration table for Base Quality Score Recalibrat... -
BaseRecalibratorSpark (BETA)
Generate recalibration table for Base Quality Score Recalibrati... -
BedToIntervalList (Picard)
Converts a BED file to a Picard Interval List. This tool provi... -
BpmToNormalizationManifestCsv (Picard)
BpmToNormalizationManifestCsv takes an Illumina BPM (Bead Pool ... -
BQSRPipelineSpark (BETA)
Both steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark ... -
BuildBamIndex (Picard)
Generates a BAM index ".bai" file. This tool creates an index ... -
BwaAndMarkDuplicatesPipelineSpark (BETA)
Takes name-sorted file and runs BWA and MarkDuplicates. Cat... -
BwaMemIndexImageCreator
Create a BWA-MEM index image file for use with GATK BWA tools ... -
BwaSpark (BETA)
Align reads to a given reference using BWA on Spark Categor... -
CalcMetadataSpark (BETA)
(Internal) Collects read metrics relevant to structural variant... -
CalculateContamination
Calculate the fraction of reads coming from cross-sample contam... -
CalculateFingerprintMetrics (Picard)
Calculate statistics on fingerprints, checking their viabilityT... -
CalculateGenotypePosteriors
Calculate genotype posterior probabilities given family and/or ... -
CalculateMixingFractions
(Internal) Calculate proportions of different samples in a pool... -
CalculateReadGroupChecksum (Picard)
Creates a hash code based on the read groups (RG). This tool c... -
CalibrateDragstrModel
estimates the parameters for the DRAGstr model Category ... -
CallCopyRatioSegments
Calls copy-ratio segments as amplified, deleted, or copy-number... -
CheckFingerprint (Picard)
Checks the sample identity of the sequence/genotype data in the... -
CheckIlluminaDirectory (Picard)
Asserts the validity for specified Illumina basecalling data. ... -
CheckPileup
Compare GATK's internal pileup to a reference Samtools mpileup ... -
CheckTerminatorBlock (Picard)
Asserts the provided gzip file's (e.g., BAM) last block is well... -
ChromosomeCounts
Counts and frequency of alleles in called genotypes (AC, AF, AN... -
CigarContainsNoNOperator
Filter out reads with CIGAR containing N operator Category ... -
CleanSam (Picard)
Cleans the provided SAM/BAM, soft-clipping beyond-end-of-refere... -
ClippingRankSumTest
Rank sum test for hard-clipped bases on REF versus ALT reads (C... -
ClipReads
Clip reads in a SAM/BAM/CRAM file Category Read Data M... -
ClusterCrosscheckMetrics (Picard)
Summary Clusters the results from a {@link CrosscheckFingerprin...