What bioinformatic tools are currently available for calling star alleles (see PharmVar) for cytochrome P450 genes such as CYP2D6 and other pharmacogenes from high throughput sequencing data? Some tools include:
Some caveats include the fact that most of these tools require whole genome sequencing data as opposed to exomes or other targeted sequencing methods. Unique alignment of short reads can also be problematic with gene family members and pseudogenes.
Are there any other tools available that are missing from the list? Has anyone had any experience using them?