The well-validated GATK software (Genome Analysis ToolKit (GATK)  has been used in conjunction with the gold-standard aligner BWA (Burrow-Wheeler Alignment)  for assembly. Prior to the alignment, each read was properly assessed and trimmed using various tools from the Picard suite (http://broadinstitute.github.io/picard). Once the alignment was performed, quality of each base has been normalized for each sample, and local realignment for suspected indels region was performed. Variant calling has been performed jointly on all samples processed together using UnifiedGenotyper from the GATK suite. We also used the ANNOVAR software to annotate variants using the most up-to-date public databases (dnSNP, REFSEQ) . The potential functional impact of mutations was predicted using Sorting Intolerant From Tolerant (SIFT), at http://sift.bii.a-star.edu.sg, and Polymorphism Phenotyping 2 (PolyPhen2), at http://genetics.bwh.harvard.edu/pph2/.