ms2gs

Using ms2gs

in the internal documentation, miguel says that one may run before

macs 200 100000 -i 3 -t .002 -r .001 -h 0.01 2>/dev/null | msformatter 2>/dev/null 

Actually, this outputs the haplotypes to std output. Correct command should be:

macs 200 100000 -i 3 -t .002 -r .001 -h 0.01 2>/dev/null | msformatter 2>/dev/null >haplo

Then, in the call to ms2gs one should specify the ms file haplo: -ms haplo.