Haploviewは今のところbiallelic markerだけ対応

Haploview can only interpret biallelic markers ― markers with greater than two alleles e.g. microsatellites) will not work correctly.

http://www.broad.mit.edu/mpg/haploview/files.php#formats
うーん、VNTRとSNPの連鎖不平衡係数を見たいのだが…SNPAlyzeかな。