heterogeneity of results
 

We are working on sequencing human exome using agilent for enrichment and GAIIx for sequencing.

We got a high heterogeneity of read profiles from a DNA sample to an other.

For example : for a given mutation, we got for 1 DNA sample a deph of 50X, for an other it will be 2X and so on.

Is it a problem due to Agilent or Illumina?

Did anybody read a paper about this issue?