Somatic CNV Model

Selecting a tumor purity and diploid coverage level (ploidy) is a key component of the somatic CNV caller. It attempts to fit the observed data, the read counts and b-allele counts, across all segments in the tumor sample, using a grid-search approach that evaluates many candidate models. A log likelihood score is emitted for each candidate. These scores are output in the *.cnv.purity.coverage.models.tsv file. The somatic CNV caller chooses the (purity, coverage) pair with the highest log likelihood, and computes several measures of model confidence based on the relative likelihood of the chosen model vs alternative models.

If the confidence in the chosen model is low, then the output VCF marks all records with a lowModelConfidence FILTER.