Joint Segmentation

First, CNV calling is performed on each sample independently. Joint segmentation then uses the copy number variable segments from each single sample analysis to derive a set of joint copy number variable segments. This set of joint segments is determined simply by taking the union of all breakpoints from the copy number variable segments of all samples. This results in the splitting of any partially overlapping segments across different samples.

Overlapping Segments

Following joint segmentation, copy number calling is again performed independently on each sample using the joint segments. Segments can be merged as with the single sample analysis, but each joint segment is emitted in the mutlisample VCF as a single entry. The quality score (QS in the VCF) from the sample's merged segment, if applicable, is used for filtering the call. Sample calls are filtered using the sample's FT field in the multisample VCF. The QUAL column of the multisample VCF is always missing (ie, "."). The FILTER column of the mutlisample VCF is "SampleFT" if none of the sample's FT fields are "PASS", and "PASS" if any of the sample's FT fields are "PASS".