Integrating with PLINK/SEQ

 In order to interpret targeted sequencing experiments with individual sample level data we suggest using PLINK/SEQ: 
PLINK/SEQ is available at http://atgu.mgh.harvard.edu/plinkseq/
 
QC metrics to look for: 

  1. HWE equilibrium test
  2. Null Genotypes
  3. Coverage as a mask