Forum: How to calculate Tajima's D and Fay & Wu's H for unphased data?
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gravatar for RoseString
3.6 years ago by
RoseString10
Atlanta
RoseString10 wrote:

Hi,

I have a small number of samples (~10) for my species of interest (non-model organism), so it's almost impossible to phase the data. I am interested in doing some site-frequency spectrum methods to detect positive selection in the genome, but they require the calculation of nucleotide diversity (pi). Is it possible to do so without phasing the data?

Thanks in advance!

ADD COMMENTlink modified 3.6 years ago by jsgounot140 • written 3.6 years ago by RoseString10
0
gravatar for jsgounot
3.6 years ago by
jsgounot140
European Union
jsgounot140 wrote:

Maybe you could use VariScan. However, I don't know if it's the best way to do it for unphased data since you will have to produce 2 sequences for each individual, and therefore randomly assign each variant to one sequence.

ADD COMMENTlink written 3.6 years ago by jsgounot140

Thanks!

Do you know any literature doing the random assignment of variants if the data is unphased?

ADD REPLYlink written 3.5 years ago by RoseString10

Just an update. I found a study using your method. They call this process 'haploidize data'.

ADD REPLYlink written 3.5 years ago by RoseString10
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