CoalescentSTR is a statistical method that estimate repeat numbers in
a microsatellite region for multiple samples from high-throughput
sequencing data. Multiple samples can be handled in one statistical
model based on coalescent theory, and accurate estimation of repeat
numbers are enabled even for microsatellite regions longer than the
length of sequence reads.

K. Kojima, Y. Kawai, N. Nariai, T. Mimori, T. Hasegawa and M.
Nagasaki. Short tandem repeat number estimation from paired-end
sequence reads by considering unobserved genealogy of multiple
individuals. Proc. 11th International Symposium on Bioinformatics
Research and Applications, volume 9096 of Lecture Notes in Computer
Science, pp.422-423, Springer Berlin Heidelberg, 2015.