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

Yu and Sun

Yu and Sun BMC Bioinformatics 2013 14:274   doi:10.1186/1471-2105-14-274

Open Data