4.0.2.0
Tool documentation for GATK release 4.0.2.0
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CNNVariantWriteTensors (EXPERIMENTAL)
Write variant tensors for training a CNN to filter variants Categor... -
CollectAlignmentSummaryMetrics (Picard)
Produces a summary of alignment metrics from a SAM or BAM file. This t... -
CollectAllelicCounts (BETA)
Collects reference and alternate allele counts at specified sites C... -
CollectBaseDistributionByCycle (Picard)
Chart the nucleotide distribution per cycle in a SAM or BAM fileThis to... -
CollectBaseDistributionByCycleSpark (BETA)
Collects base distribution per cycle in SAM/BAM/CRAM file(s). Categ... -
CollectFragmentCounts (BETA)
Collects fragment counts at specified intervals Category Cover... -
CollectGcBiasMetrics (Picard)
Collect metrics regarding GC bias. This tool collects information about... -
CollectHiSeqXPfFailMetrics (Picard)
Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory in... -
CollectHsMetrics (Picard)
Collects hybrid-selection (HS) metrics for a SAM or BAM file. This too... -
CollectIlluminaBasecallingMetrics (Picard)
Collects Illumina Basecalling metrics for a sequencing run. This tool ... -
CollectIlluminaLaneMetrics (Picard)
Collects Illumina lane metrics for the given BaseCalling analysis direc... -
CollectIndependentReplicateMetrics (Picard) (BETA)
Estimates the rate of independent replication rate of reads within a ba... -
CollectInsertSizeMetrics (Picard)
This tool provides useful metrics for validating library construction i... -
CollectInsertSizeMetricsSpark (BETA)
Collects insert size distribution information on alignment data Cat... -
CollectJumpingLibraryMetrics (Picard)
Collect jumping library metrics. This tool collects high-level metrics ... -
CollectMultipleMetrics (Picard)
Collect multiple classes of metrics. This 'meta-metrics' tool runs one... -
CollectMultipleMetricsSpark (BETA)
Runs multiple metrics collection modules for a given alignment file ... -
CollectOxoGMetrics (Picard)
Collect metrics to assess oxidative artifacts.This tool collects metric... -
CollectQualityYieldMetrics (Picard)
Collect metrics about reads that pass quality thresholds and Illumina-s... -
CollectQualityYieldMetricsSpark (BETA)
Collects quality yield metrics from SAM/BAM/CRAM file(s). Category ... -
CollectRawWgsMetrics (Picard)
Collect whole genome sequencing-related metrics. This tool computes me... -
CollectReadCounts (BETA)
Collects read counts at specified intervals Category Coverage ... -
CollectRnaSeqMetrics (Picard)
Produces RNA alignment metrics for a SAM or BAM file. This tool takes ... -
CollectRrbsMetrics (Picard)
Collects metrics from reduced representation bisulfite sequencing (Rrbs... -
CollectSamErrorMetrics (Picard)
Program to collect error metrics on bases stratified in various ways. S... -
CollectSequencingArtifactMetrics (Picard)
Collect metrics to quantify single-base sequencing artifacts. This too... -
CollectTargetedPcrMetrics (Picard)
Calculate PCR-related metrics from targeted sequencing data. This tool ... -
CollectVariantCallingMetrics (Picard)
Collects per-sample and aggregate (spanning all samples) metrics from t... -
CollectWgsMetrics (Picard)
Collect metrics about coverage and performance of whole genome sequenci... -
CollectWgsMetricsWithNonZeroCoverage (Picard) (BETA)
(Experimental) Collect metrics about coverage and performance of whole ...