Unexpected behavior!

[drdna]

Running the python version of this script using a .hap file with 42621 sites (snv file has 42621 lines), produces output haplotypes with 49028 sites! It's creating variant positions out of thin air!

Model looks like this:

*1-10 Anc1,Anc2,Admix1
100 0.5,0.5,0
10000 0,0,1
10000 0,0,1
10000 0,0,1
10000 0,0,1
10000 0,0,1
10000 0,0,1
10000 0,0,1
10000 0,0,1
10000 0,0,1

Command looks like this:

python AdmixSim2.py -i AdmixSim2 -p Admix1 -g 10 -n 100 --mut-rate 0.000001 --rec-rate 0.0000006 -o AdmixSim2.out

[Zhang-Rui-2018]

Hi! Thank you for using our software! Can I ask how long is the chromosome you are simulating?

[drdna]

Thanks for your speedy response. The chromosome is 3.66 megabases long but the number of polymorphic sites in the hap file is 42,621.

[Zhang-Rui-2018]

Hi! It makes sense since you have set the mutation rate as 0.000001, the chromosome length as 3.66Mb, so the expectation new mutations should be
chromosome length (in bp) * mutation rate * generation * #output haplotype, which is about 7k in your setting.

If you don't want new mutations, you could set the mutation rate as 0 or --no-mut in cpp version.

[drdna]

Now I see what’s happening. The program, has created a new .snv file too. I was expecting it to simply flip ones and zeroes but the actual behavior makes total sense.

[drdna]

Oh, I see what’s happening. The program, has created a new .snv file too. I was expecting it to simply flip ones and zeroes but the actual behavior makes total sense. I have changed the title of the issue to reflect my misunderstanding. I have also added some suggestions for added functionality. Mark L. Farman Professor, Department of Plant Pathology 225 Plant Science Building 1405 Veteran's Dr. University of Kentucky Lexington, KY 40546 USA tel: (859) 218-0728 fax: (859) 323-1961 On Nov 8, 2024, at 12:28 AM, Rui Zhang ***@***.***> wrote: CAUTION: External Sender Hi! It makes sense since you have set the mutation rate as 0.000001, the chromosome length as 3.66Mb, so the expectation new mutations should be chromosome length (in bp) * mutation rate * generation * #output haplotype, which is about 7k in your setting. If you don't want new mutations, you could set the mutation rate as 0 or --no-mut in cpp version. — Reply to this email directly, view it on GitHub<#2 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAYUUDJKK4NQNVTYVFXRMLLZ7RDWHAVCNFSM6AAAAABRLXY3POVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINRTG44TKNBQHA>. You are receiving this because you authored the thread.Message ID: ***@***.***>