Table 1.

Preprocessing steps in each of the four algorithms

	SOAPsnp	Atlas-SNP2	SAMtools	GATK
Version	1.03	1.2	1.1.18	1.6
Format of aligned reads	SOAP output	SAM/BAM	BAM	SAM/BAM
Duplicate reads	Penalty	Remove using Atlas-SNP-mapper	Removed	Remove using picard [41]
Reads with multiple-hit	Remove	Keep all hits	Keep all hits	Keep all hits
Quality recalibration	Yes	No	Yes	Yes
Realignment	No	No	Yes	Yes