Can Tapestri Pipeline detect CNVs?

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Although GATK/HaplotypeCaller, the genotype caller used at the pipeline level, is not optimized to detect CNVs, e.g., it requires ploidy to be defined (default = 2), using amplicon-based, high-coverage genotype data allows for the detection of copy number variants, including loss of heterozygosity (LOH).

Please review the CNV Application Note for additional information.

To install the Mosaic and analyze Tapestri data for CNV, refer to these instructions.

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