I'm new to the NGS data analysis. i am studying from the very basics of NGS how the data are analysed.
For aligning the Raw reads there many tools each one have different algorithm for example BWA works on BWT Novoalign works on Needleman wunch Mosaik works on Smith- Water man
what about the variant caller Most of the people are using GATK, SAMtools mpileup, and freebayes for the variant calling i have gone through their site but i cant find what algorithm are the using for detecting the variant where in freebayes they told that they have been using the bayesian. i want to know whether all the variant caller works on the bayesian algoritm or they are having different way of finding the variant using different algorithm