Difference between samtools and gatk algorithms

http://www.biostars.org/p/57149/

n general, samtools focuses more on a multi-purpose tool. It tends to use filters producing less bias. It produces the consensus in a more uniform (and the right) way and has the ability to infers population parameters not doable with GATK. I would say GATK focuses more on variant calling for human data. -- lh3