I need an advice concerning determining haplotypes small pedigrees/nuclear families, using next gen sequencing (whole exome) data.
I have whole exome data from families with mother, father and between one and in the best case 4 children. I also have Illumina infinium chip data on all of the individuals.
I am mainly interested in determining the haplotypes using next gen sequencing data but any robust method that may also integrate chip genotype data and whole exome data would be valuable as well. We have some experience with ENT but many other tools were mentioned before (i.e. http://biostar.stackexchange.com/questions/551/reconstruction-of-haplotypes-from-the-genotypes-on-snps ) Can you please advise on how to best approach this problem?