GenoTan is a free tool to identify length variation of microsatellites from short sequence reads. Inferring lengths of inherited microsatellite alleles with single base pair resolution from short sequence reads is challenging due to several sources of noise including PCR amplification errors, individual cell mutation, misalignment or mis-mapping caused by the repetitive nature of the microsatellites. We have developed a method using a discretized Gaussian mixture model combined with a rules-based approach to identify inherited variation of microsatellite loci from short sequence reads, which effectively distinguishes length variants from INDEL errors at homopolymers.
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Bioinformatics. 2014 Mar 1;30(5):652-9. doi: 10.1093/bioinformatics/btt595. Epub 2013 Oct 17.
Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs.
Tae H, Kim DY, McCormick J, Settlage RE, Garner HR.