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gatk-cnv

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Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

When to use

• Somatic CNV pipeline
• Germline GATK-gCNV pipeline
• Panel-of-normals construction
• AnnotateIntervals and FilterIntervals
• Allelic-count integration
• QS-based filtering
• Integrating CNV calling into GATK variant pipeline
• Calling rare germline CNVs from an exome cohort

When not to use

• Integer allele-specific copy number
• Tumor purity estimation
• Ploidy estimation
• LOH state determination
• Whole-genome-doubling status
• Targeted panel with fewer than a few hundred genes

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