The next step in the pipeline after the alignments are conducted and adjusted is to call the SNPs and genotypes. There are many programs that will do this such as the ML script that many people in the Rieseberg lab use, freeBayes, mpileup and bcftools, as well as the GATK UnifiedGenotyper. To bench mark the alignment steps in these SNP calling blog posts I used mpileup and bcftools. For example:
Rieseberg Lab Resources
RLR: Technical resources for Rieseberglers
