I used Picard CollectHsMetrics on whole exome data of 96 individuals. We used xGen® Exome Research Panel v1.0 exome capture kit.
1) In the output file ZERO_CVG_TARGETS_PCT ranges from 37-41. The definition of "ZERO_CVG_TARGETS_PCT" is "The fraction of targets that did not reach coverage=1 over any base". Does that mean that I do not have any coverage in approximately 40% of my intended target bases? Is that normal?
2) PCT_TARGET_BASES_20X ranges from 0.92-0.95. The definition of "PCT_TARGET_BASES_20X" is "The fraction of all target bases achieving 20X or greater coverage". How is it possible to have at least 20X coverage in 93% of all target bases while having zero coverage in 40% of targets?
I think I misinterpreted something here. I was wandering if someone could shed light on it. Thanks in advance.
