Interpretation of results

[GoogleCodeExporter]

Hi,

I ran the simulation as suggested in the readme file
./macs 100 1e6 -T -t .001 -r .001 -h 1e2 -R inputfiles/hotspot.txt -F 
inputfiles/ascertainment.txt 0 2>trees.txt | ./msformatter > haplotypes.txt

Then I look up  haplotypes.txt.

I get lines of kind:
//
[48]((13:0.641735,(((((((75:0.00122728,11:0.00122728):0.000699119,(77:0.00042199
2,0:0.000421992):0.00150441):0.0043
...

what does the number in square brackets mean?

Further on I see haplotypes
110011111000001010001000000001000011011011000000000000011000001...

what do 0s and 1s mean? 
Why are there exactly 2816 symbols in each line?

Kind regards
Dominik

Original issue reported on code.google.com by d.glod...@gmail.com on 29 Aug 2012 at 5:33

[GoogleCodeExporter]

Hi Dominik,

The [48] says that this current tree spans 48 base pairs. Note that trees are 
generated from the left end of the simulated region to the right end.  The 
haplotypes represent the alleles ordered from the left end to the right end of 
the region.  There were 2816 sites in your case.  Let me know if this answers 
your question.

Gary

Original comment by gche...@gmail.com on 29 Aug 2012 at 5:47

• Changed state: Accepted
• Added labels: Type-Task
• Removed labels: Type-Defect

[GoogleCodeExporter]

Why are there exactly 2816 sites? Is it because 2816 distinct mutations 
occurred?

Original comment by d.glod...@gmail.com on 29 Aug 2012 at 5:49

[GoogleCodeExporter]

That's correct.

Original comment by gche...@gmail.com on 29 Aug 2012 at 5:54

[GoogleCodeExporter]

I am closing this old issue.

Original comment by gche...@gmail.com on 14 Nov 2012 at 6:13

• Changed state: Done