We have developed a protocol for class I HLA genotyping using 454 sequencing technology and an algorithm for calling HLA genotypes from next-generation sequence data. This was described in a paper in BMC Genomics. The algorithm is part of the Genome Analysis Toolkit (GATK).

We have developed MANTEL, a tool for performing a meta-analysis of GWAS data sets, including detailed QC checks for individual GWAS data sets and generation of regional association plots. You can download it here (caveat: this tarball is a 500 MB file as it contains many auxiliary files like HapMap, RefSeq, dbSNP). You can download here the documentation.