MsToGlf

For the Korneliussen2013 paper, we simulated data according to genotypes simulated from ms/msms output. For this we used the msToGlf program found in the 'misc/' subfolder of the angsd tar ball.

Sorry about the total lack of information for this program.

Brief Overview

 ./msToGlf 
Probs with args, supply -in -out
also -err -depth -depthFile -singleOut -regLen -nind

-in ms/msms outputfilename

-out prefix output filename

-regLen [int] Number of base pairs the ms/msms output is supposed to represent

-singleOut [zero or one] ms/msms can generate multiple replicates of the same scenario '-singleOut 1' will generate a single output file

-depth average sequencing depth

-nind Number of individuals in the ms/msms file

-err errorrate, a value 0.005 corresponds to a 0.5% errorrate.

-depthFile filename, This is useful if you want to force a different mean depth between individuals