Stacks haploid and diploid.

[mig...@uji.es]

Hi all stacks-users, 

Can Stacks work with haploid and diploid samples mixed in a same denovo_map run-analysis?

Thanks!

Miquel

[mig...@uji.es]

any idea?

[Ryan Waples]

Hey Miquel, 

My sense is that yes, it can.  Stacks is built for (and assumes) diploidy, but it can deal with haploids decently well.  It will treat all of your samples the same regardless of their true ploidy, as there is no way to tell it the ploidy (notice there is no ploidy flag anywhere).

You will however need to think about how interpret the genotypes assigned to diploids and haploids - what does a heterozygote call in a haploid mean? and you may need to sort the haploids and diploids back out for subsequent analyses as well

Good luck!

-ryan 

any idea?

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[BeeBern]

Hi all

I got the same question as well for bumblebee data that contain a couple of populations.  A few populations have e.g. 4 haploid (male) and /or 8 diploid (female) samples.  As pointed out, there is no ploidy flag anywhere. Even though I have read this, it seems that the authors haven't confirmed the discussion of this conversation and  I am still not sure if I can use this program to calculate population pairwise Fst?

Thanks

Yuanzhen

[BeeBern]

It seemed that 'stacks populations' does not consider haploid genotype when two pairwise populations have both diploid and haploid samples.

[van_Hommel]

So from your experience, can you recommend a way how to process in Stacks halopoid and diploid individuals in a mixed sample, particularly how to calculate pairwise Fst?

Thanks Somm