Hello Forum,

What pipelines are available for exome sequencing analysis? Thanks for information.
In addition to Ram's excellent answer, have a look at [bcbio-nextgen][1] and [Brad Chapman's blog][2]. The former demonstrates some effective methods for alignment and processing, the later describes a good number of comparisons that you should be familiar with if you want to really get into variant calling pipelines.

 [1]: https://bcbio-nextgen.readthedocs.org/en/latest/
 [2]: http://bcb.io/