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In the current high-throughput genomics era, efficient and accurate analysis of large-scale whole-genome sequencing (WGS) data constitutes a computational bottleneck. Johnston et al. (1) introduce the PEMapper/PECaller software package for short-read WGS alignment and variant calling, promising faster analyses with reduced output file sizes and “nearly identical (or better)” variant calling accuracy compared with the de facto standard Burrows–Wheeler aligner/Genome Analysis Toolkit (BWA/GATK) best-practices pipeline (2). However, we cannot confirm this promised BWA/GATK-like accuracy of PEMapper/PECaller, and there are other pipelines offering ultrafast WGS data analyses with small disk footprints, as we show in this correspondence.To assess sensitivity/recall, precision, computation time, and disk footprint of four corresponding pipelines, we performed alignment and variant calling for the reference short-read WGS data of NA12878 and the Ashkenazim trio (3, 4). The four pipelines included the downloadable PEMapper/PECaller (1) and BWA/GATK (2) as well as the commercially available Isaac (5) and GENALICE MAP (genalice.com) software packages (versions and settings specified in Fig. 1). To largely reduce systematic errors and alignment artifacts, we limited our benchmarking of whole-genome variant … [↵][1]2To whom correspondence should be addressed. Email: matyas{at}genetikzentrum.ch. [1]: #xref-corresp-1-1

Need for speed in accurate whole-genome data analysis: GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac