Hello all,

I have a GWAS cohort and a WGS cohort that is a subset of the GWAS cohort.

I have identified all the lead SNPs from the GWAS data (larger n) and have defined linkage disequilibrium around each lead SNP in the study.

Further, I have phased the WGS genomes. As such, I can determine the variants that are in phase, or not in phase, with the lead SNPs in the study.

Right now, it is my intention to do this by parsing the VCF files, then reformatting into SKAT-O format. However, my question is, *are there existing workflows that port phased genomes directly into any rare variant association tool, or, is one or more of these steps DIY?*

For clarity, what I mean by rare variant association tools is roughly summarized by [the Lee / Lin review paper in AJHG][1]

 [1]: http://www.ncbi.nlm.nih.gov/pubmed/24995866
I wrote a script to do exactly this: 

https://gist.github.com/brentp/4ec866b5ab3dd4e7bc46

It parses the VCF in python and sends the haplotype blocks to R using [pyper][1]. It can be a start for the parsing/creating haplotypes or you can use it as-is to get p-values from SKAT.

There are a lot of methods for testing haplotypes, but I think [this poster][2] does a nice job comparing.

 [1]: https://pypi.python.org/pypi/PypeR/1.1.0
 [2]: http://srcos2014.blogs.rice.edu/files/2014/07/AnandaDatta.pdf