Preprocess your data using

SNiPloid assumes that short reads datasets (i.e. samples) derived from distinct accessions (diploid or polyploid) have been separately preprocessed as described here.
Run SNiPloid to compare SNPs between accessions.
SNiPloid compares SNPs in overlapping user-defined interval

Run SNiPloid on-line or
Download SNiPloid executable
Exploit SNiPloid results

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