Analysing MiSeq data with SureCall

[rcran]

Hi everyone!

I was wondering if anyone on here has used SureCall for detecting low level mutations in a sample?
I'm a bit confused about the variety of parameters which can be changed in SureCall and the lack of a software manual isn't good!
If anyone is carrying out any similar research I'd love to hear which parameters you have changed to optimise the program.

one aspect of my current project is investigating the ability of next gen sequencing to detect low level clones in leukaemia samples.

I'm using a custom HaloPlex target enrichment, MiSeq and SureCall.

Any help would be great.
Cheers!