Checks if all fingerprints within a set of files appear to come from the same individual. The fingerprints are calculated initially at the readgroup level (if present) but can be "rolled-up" by library, sample or file, to increase power and provide results at the desired resolution. Regular output is in a "Moltenized" format, one row per comparison. In this format the output will include the LOD score and also tumor-aware LOD score which can help assess identity even in the presence of a severe LOH sample with high purity. A matrix output is also available to facilitate visual inspection of crosscheck results. A separate CLP, ClusterCrosscheckMetrics, can cluster the results as a connected graph according to LOD greater than a threshold.
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