Hi,

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

I found these are the major difference between GATK and Samtools

 1. Preprocess of alignment" GATK drops reads with low mapping quality , but samtools uses all reads by default.
 2. SNP genotype likelihood model: GATK assumes sequencing errors are independent while samtools believes the second error comes at a higher chance.Indel genotype likelihood model. This is one of the major differences between samtools and GATK. Samtools model is derived from BAQ. GATK's model was derived from Dindel's model.
 3. Samtools uses hand-tuned filters, while GATK learns filters from data. Of course GATK's approach is more convenient and powerful at least for human variant calling where you have enough data to train the model and you do not need non-polymorphic sites
 4. Other GATK specific features: haplotype caller, indel realignment among many others.
 5. Other samtools specific features: genotype-free analysis, physical phasing and so on.