Table 3.

Program memory allocation and runtimes for pooled BAM files of 4, 8, and 16 ClinSeq samples, 35.1× average coverage each

Program	CPU Hours per BAM file	Memory Used/Provided
CRISP	<2 h	<150 Mb Used
SNVer	1 - 5 h	4 - 8 Gb Provided
LoFreq	1 - 5 h	~150 Mb Used
VarScan	2 - 5 h	6-8 GB Provided
GATK	8 h - +7 days	4 - 20 Gb Provided

Java programs required users to specify memory restrictions. Programs written in C were memory efficient and ran relatively quickly