Variant calling for haloplex data.

[michelle.lupton]

I am carrying out variant calling on sequencing data for candidate regions selected using an Agilent Haloplex custom panel.

There is quite a large variation in depth of coverage between amplicons. Would people advise to filter out variant calls for amplicons with low depth across all samples. What would be the recommended minimum mean depth?

We are carrying out variant calling using GATK, applying the recommended hard filtering. Are there any differences in the filtering required for Haloplex data, compared to exome sequencing?

Any suggestions greatly appreciated!