v1.0

Completed Exome-seq pipeline based on GATK best practices:

Mapping:
http://gatkforums.broadinstitute.org/gatk/discussion/6483/how-to-map-and-clean-up-short-read-sequence-data-efficiently

Marking Duplicates:
http://gatkforums.broadinstitute.org/gatk/discussion/6747/how-to-mark-duplicates-with-markduplicates-or-markduplicateswithmatecigar

Realignment around indels:
http://gatkforums.broadinstitute.org/gatk/discussion/2800/howto-perform-local-realignment-around-indels

Base Quality Score Recalibration:
http://gatkforums.broadinstitute.org/gatk/discussion/2801/howto-recalibrate-base-quality-scores-run-bqsr