The PCAWG ground truth files contain minor and major absolute copy number. A minor allele fraction (MAF) can be easily backed out of this, per segment.
An evaluation should be added that looks at the concordance of the GATK CNV MAF from ModeledSegments with the derived MAF from the PCAWG ground truth. Similar to the WGS BpConcordance test we currently have, except with MAF, instead of CR.
The PCAWG ground truth files contain minor and major absolute copy number. A minor allele fraction (MAF) can be easily backed out of this, per segment.
An evaluation should be added that looks at the concordance of the GATK CNV MAF from ModeledSegments with the derived MAF from the PCAWG ground truth. Similar to the WGS BpConcordance test we currently have, except with MAF, instead of CR.