search

MEEIBioinformaticsCenter / phy-mer

phy-mer
10 stars 6 forks source link

Output with defining SNPs #1

Closed nuin closed 9 years ago

nuin commented 9 years ago

Not exactly an issue, but a question: are the polymorphisms output when the --def-snps option is used are only the polymorphisms that define the resulting haplogroup, or all SNPs found on the particular genome?

danielnavarrogomez commented 9 years ago

Hello,

Since Phy-Mer doesn't use a reference sequence, is not able to "call" snps.

Answering your question, the polymorphisms that you get from the option "--def-snps" are the polymorphisms that define the resulting haplogroup, not the snps on the input.

If you need a deeply analysis of the polymorphisms, I recommend you to check https://mseqdr.org "the Mitochondrial Disease Sequence Data Resource Consortium", you will find tools on it that may help you.

Best,

Daniel.

nuin commented 9 years ago

Thanks, I have been checking your code, and trying to find the best option to align NCBI genomes to the rCRS. I think the best option would be to use Blast and get the polymorphic sites from a table result.

I will close the issue and will add any questions I have on new "issues".