clustering snps for haplogroup assignment

Question

[willing_mh]

From a set of reads (mitochondial in this case ) that have been aligned to a reference sequence I have the corresponding list of mutations, per read. As part of haplogroup assignment/verification I'd like to cluster the mutations to see which sets of linked mutations occur most frequently. Any suggestions for software for doing this?

[Shicheng Guo]

Hi, did you find the curated list. Can you share me a copy. Thanks.