Ploidy Caller

The Ploidy Caller uses the per contig median coverage values from the Ploidy Estimator to detect aneuploidy and chromosomal mosaicism in a human germline sample from whole genome sequencing data.

The Ploidy Caller runs by default except in the following circumstances:

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The Ploidy Estimator cannot determine if the input data is from whole genome sequencing. For example, data from exome or targeted sequencing.

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The reference genome does not contain the expected 22 autosomes and two allosomes for humans.

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There is no germline sample. For example, tumor-only analysis.