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Table 3 Program memory allocation and runtimes for pooled BAM files of 4, 8, and 16 ClinSeq samples, 35.1× average coverage each

From: Evaluation of variant detection software for pooled next-generation sequence data

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

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

ISSN: 1471-2105

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