GATK Team
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Activity overview
Latest activity by GATK Team-
GATK Team created an article,
QualityYieldMetrics
Back to Tool Docs Index Metrics Category Metrics Overview A set of metrics used to describe the general quality of a BAM file This table summar...
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GATK Team created an article,
CheckPileup
Compare GATK's internal pileup to a reference Samtools mpileup Category Diagnostics and Quality Control Overview Compare GATK's internal pileup to a reference Samt...
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GATK Team created an article,
CreateSomaticPanelOfNormals (BETA)
Make a panel of normals for use with Mutect2 Category Variant Filtering Overview Create a panel of normals (PoN) containing germline and artifactual sites for use ...
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GATK Team created an article,
FilterVariantTranches
Apply tranche filtering Category Variant Filtering Overview Apply tranche filtering to VCF based on scores from an annotation in the INFO field. The annotation ca...
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GATK Team created an article,
CalibrateDragstrModel
estimates the parameters for the DRAGstr model Category Short Variant Discovery Overview Estimates the parameters for the DRAGstr model for an input sample. ...
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GATK Team created an article,
ASEReadCounter
Generates table of filtered base counts at het sites for allele specific expression Category Coverage Analysis Overview Calculate read counts per allele for allele...
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GATK Team created an article,
PrintReadsSpark
PrintReads on Spark Category Read Data Manipulation Overview Additional Information Read filters This Read Filter is automatically applied...
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GATK Team created an article,
CountBasesSpark
Counts bases in the input SAM/BAM Category Coverage Analysis Overview Calculate the overall number of bases SAM/BAM/CRAM file Input A single BAM file ...
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GATK Team created an article,
CountReadsSpark
Counts reads in the input SAM/BAM Category Coverage Analysis Overview Calculate the overall number of reads in a SAM/BAM file Input A single BAM file ...
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GATK Team created an article,
ReadAnonymizer (EXPERIMENTAL)
Replace bases in reads with reference bases. Category Other Overview Replace bases in reads with reference bases. Used to anonymize reads with information from t...