Gene flow estimation with 2 haplotypes?

[arundurvasula]

Hi,

Is it possible to run msmc with the -P option where there are two haplotypes, each from a different subpopulation? It only seems to work so far with 4+ haplotypes.

Thanks!

[stschiff]

Hello Arun,

Yes, of course you can run it on 2+2 haplotypes. That’s the standard case for cross-population analysis, as shown for example in Figure 4 of our article (Schiffels and Durbin, 2014).

You would input a standard file with 4 haplotypes, and use „-P 0,0,1,1“ to denote the two subpopulations. You can also use an input file with more haplotypes and subselect some using the „-I“ option.

Stephan

P.S. Please note the new google-group on MSMC, CC’d.

Am 27.10.2015 um 14:51 schrieb Arun Durvasula notifications@github.com:

Hi,

Is it possible to run msmc with the -P option where there are two haplotypes, each from a different subpopulation? It only seems to work so far with 4+ haplotypes.

Thanks!

—
Reply to this email directly or view it on GitHub #17.

[stschiff]

Hi Stephan,

Sorry, I was unclear. I meant 1+1 haplotypes where there are two total
haplotypes in the input file, each one from a different subpopulation.

Thanks!
Arun

On Wednesday, October 28, 2015 at 8:30:24 AM UTC+1, Stephan Schiffels wrote:

Hello Arun,

Yes, of course you can run it on 2+2 haplotypes. That’s the standard case
for cross-population analysis, as shown for example in Figure 4 of our
article (Schiffels and Durbin, 2014).

You would input a standard file with 4 haplotypes, and use „-P 0,0,1,1“ to
denote the two subpopulations. You can also use an input file with more
haplotypes and subselect some using the „-I“ option.

Stephan

P.S. Please note the new google-group on MSMC, CC’d.

Am 27.10.2015 um 14:51 schrieb Arun Durvasula <notifi...@github.com
javascript:>:

Hi,

Is it possible to run msmc with the -P option where there are two
haplotypes, each from a different subpopulation? It only seems to work so
far with 4+ haplotypes.

Thanks!

—
Reply to this email directly or view it on GitHub
#17.

[stschiff]

In that case you can just run it as with a normal diploid individual and plot the inverse population size as coalescence rate. But you don’t get estimates for the coalescence rates within each population, so you cannot make the relative cross coalescence rate plot I have in the papers.
Your case is very similar to what in Li and Durbin was done with the haploid X chromosomes (the „pseudo-diploid“ individuals).

Stephan

Am 28.10.2015 um 10:34 schrieb adurvasula adurvasula@ucdavis.edu:

Hi Stephan,

Sorry, I was unclear. I meant 1+1 haplotypes where there are two total haplotypes in the input file, each one from a different subpopulation.

Thanks!
Arun

On Wednesday, October 28, 2015 at 8:30:24 AM UTC+1, Stephan Schiffels wrote:
Hello Arun,

Yes, of course you can run it on 2+2 haplotypes. That’s the standard case for cross-population analysis, as shown for example in Figure 4 of our article (Schiffels and Durbin, 2014).

You would input a standard file with 4 haplotypes, and use „-P 0,0,1,1“ to denote the two subpopulations. You can also use an input file with more haplotypes and subselect some using the „-I“ option.

Stephan

P.S. Please note the new google-group on MSMC, CC’d.

Am 27.10.2015 um 14:51 schrieb Arun Durvasula <notifi...@github.com javascript:>:

Hi,

Is it possible to run msmc with the -P option where there are two haplotypes, each from a different subpopulation? It only seems to work so far with 4+ haplotypes.

Thanks!

—
Reply to this email directly or view it on GitHub #17.

You received this message because you are subscribed to the Google Groups "msmc-popgen" group.
To unsubscribe from this group and stop receiving emails from it, send an email to msmc-popgen+unsubscribe@googlegroups.com mailto:msmc-popgen+unsubscribe@googlegroups.com.
To post to this group, send email to msmc-popgen@googlegroups.com mailto:msmc-popgen@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/msmc-popgen/08d65e60-f62b-48be-a896-bd53ffb790f6%40googlegroups.com https://groups.google.com/d/msgid/msmc-popgen/08d65e60-f62b-48be-a896-bd53ffb790f6%40googlegroups.com?utm_medium=email&utm_source=footer.
For more options, visit https://groups.google.com/d/optout https://groups.google.com/d/optout.

[arundurvasula]

Okay, that makes sense. Thank you!