4.0.1.0
Tool documentation for GATK release 4.0.1.0
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BaseQuality
Median base quality of bases supporting each allele (MBQ) Category ... -
BaseQualityRankSumTest
Rank sum test of REF versus ALT base quality scores (BaseQRankSum) ... -
BaseRecalibrator
Generates recalibration table for Base Quality Score Recalibration (BQS... -
BaseRecalibratorSpark (BETA)
Generate recalibration table for Base Quality Score Recalibration (BQSR... -
BaseRecalibratorSparkSharded (EXPERIMENTAL)
BaseRecalibrator on Spark (experimental sharded implementation) Cat... -
BedToIntervalList (Picard)
Converts a BED file to a Picard Interval List. This tool provides easy... -
BQSRPipelineSpark (BETA)
Both steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark Catego... -
BuildBamIndex (Picard)
Generates a BAM index ".bai" file. This tool creates an index file for... -
BwaAndMarkDuplicatesPipelineSpark (BETA)
Takes name-sorted file and runs BWA and MarkDuplicates. Category ... -
BwaMemIndexImageCreator
Create a BWA-MEM index image file for use with GATK BWA tools Categ... -
BwaSpark (BETA)
BWA on Spark Category Read Data Manipulation Overview... -
CalcMetadataSpark (BETA)
(Internal) Collects read metrics relevant to structural variant discove... -
CalculateContamination
Calculate the fraction of reads coming from cross-sample contamination ... -
CalculateFingerprintMetrics (Picard)
Calculate statistics on fingerprints, checking their viabilityThis tool... -
CalculateGenotypePosteriors
Calculate genotype posterior probabilities given family and/or known po... -
CalculateMixingFractions
(Internal) Calculate proportions of different samples in a pooled bam ... -
CalculateReadGroupChecksum (Picard)
Creates a hash code based on the read groups (RG). This tool creates a... -
CallCopyRatioSegments (BETA)
Calls copy-ratio segments as amplified, deleted, or copy-number neutral... -
CheckFingerprint (Picard)
Checks the sample identity of the sequence/genotype data in the provide... -
CheckIlluminaDirectory (Picard)
Asserts the validity for specified Illumina basecalling data. This too... -
CheckPileup
Compare GATK's internal pileup to a reference Samtools mpileup Cate... -
CheckTerminatorBlock (Picard)
Asserts the provided gzip file's (e.g., BAM) last block is well-formed;... -
ChromosomeCounts
Counts and frequency of alleles in called genotypes (AC, AF, AN) Ca... -
CigarContainsNoNOperator
Filter out reads with CIGAR containing N operator Category Rea... -
CleanSam (Picard)
Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alig... -
ClippingRankSumTest
Rank sum test for hard-clipped bases on REF versus ALT reads (ClippingR... -
ClipReads
Clip reads in a SAM/BAM/CRAM file Category Read Data Manipulat... -
ClusterCrosscheckMetrics (Picard)
Summary Clusters the results from a {@link CrosscheckFingerprints} run ... -
CNNScoreVariants (EXPERIMENTAL)
Apply a Convolutional Neural Net to filter annotated variants Categ... -
CNNVariantTrain (EXPERIMENTAL)
Train a CNN model for filtering variants Category Variant Filt...