4.2.2.0
Tool documentation for GATK release 4.2.2.0
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CNNScoreVariants
Apply a Convolutional Neural Net to filter annotated variants ... -
CNNVariantTrain (EXPERIMENTAL)
Train a CNN model for filtering variants Category Vari... -
CNNVariantWriteTensors (EXPERIMENTAL)
Write variant tensors for training a CNN to filter variants ... -
CollectAlignmentSummaryMetrics (Picard)
Produces a summary of alignment metrics from a SAM or BAM file.... -
CollectAllelicCounts
Collects reference and alternate allele counts at specified sit... -
CollectArraysVariantCallingMetrics (Picard)
CollectArraysVariantCallingMetrics takes a Genotyping Arrays VC... -
CollectBaseDistributionByCycle (Picard)
Chart the nucleotide distribution per cycle in a SAM or BAM fil... -
CollectBaseDistributionByCycleSpark (BETA)
Collects base distribution per cycle in SAM/BAM/CRAM file(s). ... -
CollectDuplicateMetrics (Picard)
Collect Duplicate metrics from marked file. This tool only coll... -
CollectGcBiasMetrics (Picard)
Collect metrics regarding GC bias. This tool collects informati... -
CollectHiSeqXPfFailMetrics (Picard)
Classify PF-Failing reads in a HiSeqX Illumina Basecalling dire... -
CollectHsMetrics (Picard)
Collects hybrid-selection (HS) metrics for a SAM or BAM file. ... -
CollectIlluminaBasecallingMetrics (Picard)
Collects Illumina Basecalling metrics for a sequencing run. Th... -
CollectIlluminaLaneMetrics (Picard)
Collects Illumina lane metrics for the given BaseCalling analys... -
CollectIndependentReplicateMetrics (Picard) (EXPERIMENTAL)
Estimates the rate of independent replication rate of reads wit... -
CollectInsertSizeMetrics (Picard)
Collect metrics about the insert size distribution of a paired-... -
CollectInsertSizeMetricsSpark (BETA)
Collects insert size distribution information on alignment data... -
CollectJumpingLibraryMetrics (Picard)
Collect jumping library metrics. This tool collects high-level ... -
CollectMultipleMetrics (Picard)
Collect multiple classes of metrics. This 'meta-metrics' tool r... -
CollectMultipleMetricsSpark (BETA)
Runs multiple metrics collection modules for a given alignment ... -
CollectOxoGMetrics (Picard)
Collect metrics to assess oxidative artifacts.This tool collect... -
CollectQualityYieldMetrics (Picard)
Collect metrics about reads that pass quality thresholds and Il... -
CollectQualityYieldMetricsSpark (BETA)
Collects quality yield metrics from SAM/BAM/CRAM file(s). C... -
CollectRawWgsMetrics (Picard)
Collect whole genome sequencing-related metrics. This tool com... -
CollectReadCounts
Collects read counts at specified intervals Category C... -
CollectRnaSeqMetrics (Picard)
Produces RNA alignment metrics for a SAM or BAM file. This too... -
CollectRrbsMetrics (Picard)
Collects metrics from reduced representation bisulfite sequenci... -
CollectSamErrorMetrics (Picard)
Program to collect error metrics on bases stratified in various... -
CollectSequencingArtifactMetrics (Picard)
Collect metrics to quantify single-base sequencing artifacts. ... -
CollectTargetedPcrMetrics (Picard)
Calculate PCR-related metrics from targeted sequencing data. Th...