Table 6

Computing performance of major functions using 23 exome sequencing samples on a 16 CPU workstation

Script

Function

#CPU

Peak RAM

(Gb)

Time

Notes


exon_qc

quality control

1

6

10-20 min

Per sample


sam2wig

generate wig file

1

2

20-50 min

Per sample


sam2pileup

generate pileup file

1

3-7

1-4 hours

Per sample


snp

annotate and filter snp and indels

1

4

2-8 min

Per sample


rpkm

quantify coverage on gene model

1

4

4-16 min

Per sample


cnv

copy number variation

1

4

5 min

Per sample


genotyping

genotyping file across samples

1

8

4 hour

Across 23 samples


phenotyping

coverage (expression) across samples

1

5

10 min

Across 23 samples


eqtl -m cis

Cis- EQTL

1

3

1 hour

1000 genome data


eqtl -m trans

Trans-EQTL

16 *

3

7 days

1000 genome data


Deng BMC Bioinformatics 2011 12:267   doi:10.1186/1471-2105-12-267

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