#14 converting output to ms format

[Anonymous]

Dear all,

I want to simulate 5 extant populations + 1 ancient population and get the allele frequencies for all of them. I've run sfs_code (SEED = -194836275) with the following command and all went good:

./sfs_code 6 1 -t 0.0000472 -L 10000 100 --linkage g 0.5 --sampSize 50 50 50 50 50 1 -TS 0 0 1 -TS 1.452 1 2 -TS 1.96 2 3 -TS 1.96 2 5 -TE 1.96 5 -TS 2.212 3 4 -TE 3.16 --popFreq data.freq -o data.sfs

afterwards, I tried converting it to ms format:

./convertSFS_CODE data.sfs --ms F data.ms

and, even thnough it converted the file just fine, there are some strange issues:
- on the ms file there are sites with the same position:
"positions: 0.000357 0.000877 0.001862 0.001862 0.001862 0.002131 0.002604 0.002631 ..."
I thought it could be a precision issue and so changed the fprintf precision on the source code but it didn't help. Is this a bug?

• on the ms file there are 1547 segsites but, on the popFreq file there are 2107 mutations. I'd expect some differences since some mutations ocurr on the burn-in and there can be recurrent mutations but I only found 79 and 4 of those, respectively. What are the other mutations? Is there a way to get just the pop freqs of segregating sites?

thanks in adv,

PS - find attached the .sfs and .ms files