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Runtime, peak RAM, and disk use in GATK4 (Java/Intel mode) vs. elPrep 5 (filter/sfm mode). The elPrep filter mode is 11 to 15x faster than the GATK modes, using ±4x more RAM, and less than 15% of the disk space GATK uses. The elPrep sfm mode is 6 to 7.5x faster than GATK4, uses roughly half as much RAM, and uses less than half of the disk space GATK uses. The output of elPrep 5, i.e., BAM, VCF, and metrics, is identical to the output of GATK.
