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DepthOfCoverage in parallel mode does not actually run in parallel
I've been using DepthOfCoverage tool for coverage estimation for human WGS data, which was aligned with BWA MEM, filtered using samtools and passed through MarkDuplicates. I tried to run DepthOfCoverage in parallel mode using
--omitIntervalStatistics and in a single-threaded mode. All the data is stored on an SSD and being processed on a server with 12 actual cores. Surprisingly, the speed of data processing as reported by ProgressMeter is two times faster in a single-threaded mode (15 sec per 1 million sites vs 30 sec). I understand the limitations of I/O, but it is confusing when compared with some other GATK (non-Spark) tools which are actually able to process data in
-nct mode with reading/writing.
Does this behaviour actually look like as it is supposed to? Any comment would be greatly appreciated.