genetic position in .snp file about admixtools HOT 3 CLOSED

1. 0 is OK in my software and programs like convertf fill in a distance
   table using physical position
   (1 morgan = 100M bases). In my own work I have software to fill in
   distance with the Oxford map,
   but this code is not released.

Thus most software will run OK but for careful work you should find a way
to fill in the table.
Nick

On Sun, Nov 6, 2016 at 8:25 PM, Shubham Saini [email protected]
wrote:

I am working with VCF files. I am able to convert between different
formats (VCF <--> PLINK <--> EIGENSTRAT). But the .snp file generated in
this process has genetic position values all 0. Is there any way I can
populate these? Perhaps using the genetic maps files?

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So I'm working with ROLLOFF. I believe most analysis depend on genetic positions and bins sizes in cM. How do you think my analysis would be affected if I were to use genetic position values approximated from the physical positions?

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I've had good luck with doing that, but you ought to use a genetic map if
possible. What is your genotype array? By the way, look into ALDER.
Similar math and much faster.

N

On Sun, Nov 6, 2016 at 10:15 PM, Shubham Saini [email protected]
wrote:

So I'm working with ROLLOFF. I believe most analysis depend on genetic
positions and bins sizes in cM. How do you think my analysis would be
affected if I were to use genetic position values approximated from the
physical positions?

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