Table 2

Metrics considered in calling SNPs by each of the four algorithms
SOAPsnp Atlas-SNP2 SAMtools GATK-UGT
Quality score Recalibrated Raw Recalibrated Recalibrated
Machine cycle Yes Yes No Yes
Allele type Yes No No Yes
Duplication level Penalty in quality score No No No
Swap-base No Yes No No
MNP events No Yes No No
NQS No Yes No No
Coverage variation No Yes No No
Base dependency Yes No Yes No
Strand independency No NO Yes No

Yu and Sun

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

Open Data