SNP calling using pooled RNA-seq data

Hello,

First of all, thank you for your detailed best practice pipeline for SNP calling from RNA-seq data.

I have pooled RNA seq data which I need to call SNP from. Each library consists of a pooled sample of 2-3 individuals of the same sex-tissue combination.

I was wondering if Haplotype caller can handle SNP calling from pooled sequences or is it better if I use FreeBayes?

I understand that these results come from experimenting with the data but it would be great if you could share your experiences with me on this.

Cheers,
Homa