What is the basic difference between variant callers (haplotype calling). We have callers like, GATK, Freebayes, Vardict, Platypus, etc. Each callers have their own sensitivity to call variants as per to mapped reads. What more basic difference they have ? For fetching all the variants (possibly) which caller should be used in Whole Exome Sequencing and Clinical Exome Seq. ?
I am looking into literature as well, seek some advise to explore in more better way.
Regards and thanks.