Axiom Exome-Chip Ld Aware Genotype Calling

Question

[kapoormaan]

I am looking for some program which can call rare and low frequency SNPs in Axiom Exome array using 1000 genome as reference. We are very much concerned about QC issues related to very low frequency SNPs and probably LD aware calling can be of help regarding this issue. It would be great if someone can suggest a good LD aware caller and QC workflow for the axiom Exome chip data.

Thanks,

Maan