Table 1.

Summary of parameter settings used for SNP calling and filtering for the selected SNP tools

All tools used default settings or suggested settings based on either direct communication with its author, or technical support, or forum communication. Although 0.99 is the default setting for VQSR, two thresholds of the VQSR step of GATK (0.99 and 0.90) were used to assess the robustness of the tools and were designated as GATK0.99 and GATK0.90; samtools_group was designated for SAMtools calls using pooled samples simultaneously, whereas samtools_individual designated as the SAMtools calls using individual samples one at a time. UG: Unified genotyper from GATK.