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Hello,
In one of our whole genome re-sequencing project, we have dozens of diploid accessions and about 20 multiploid ones. I have finished the population SNPs calling, however, when I am trying to use the data to construct a phylogenetic tree, I get an obstacle:
How should I handle the heterogeneous SNPs in multiploid accessions like 0/0/1/1/1/1/1/1:15,43:58, and 0/0/0/0/0/0/0/1/1/1:48,19:67 ? Can I take them all as the same as hetero site (GT: 0/1) in diploid accessions ?
I have tried to using SNP showing homogeneous genotype in each accession to bypass this issue, but the homo SNPs seems to be relatively conserved, and the tree can't tell from all the accessions finally.
Any suggestions and references are highly appreciated. Thanks in advance.
Sheng
In one of our whole genome re-sequencing project, we have dozens of diploid accessions and about 20 multiploid ones. I have finished the population SNPs calling, however, when I am trying to use the data to construct a phylogenetic tree, I get an obstacle:
How should I handle the heterogeneous SNPs in multiploid accessions like 0/0/1/1/1/1/1/1:15,43:58, and 0/0/0/0/0/0/0/1/1/1:48,19:67 ? Can I take them all as the same as hetero site (GT: 0/1) in diploid accessions ?
I have tried to using SNP showing homogeneous genotype in each accession to bypass this issue, but the homo SNPs seems to be relatively conserved, and the tree can't tell from all the accessions finally.
Any suggestions and references are highly appreciated. Thanks in advance.
Sheng