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.

This program assumes diploid samples.

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

Output format

The program will dump a binary compressed file. It will calculate all 10 possible genotype likelihoods for each individual for all sites. The genotypes are in the order AA,AC,AG,AT,CC,CG,CT,GG,GT,TT. These are encoded as ctype 'double'. So the size requirements for a single site for N individuals are 'N*10*sizeof(double)'.

Examples

Standard neutral model

This ms/msms command will generate haplotypes assuming human recombination/mutation rates for a 1mb region. We will make 50 haplotypes (25 diploids) and do 14 repetitions.

msms -ms 50 14 -t 900 -r 400 -oTPi 0.05 0.05 -oAFS >msoutput

Now we will simulate genotype likelihoods assuming an errorate of 1.5% and a sequencing depth of 8x, but only for the variable/informative sites contained in the msoutputfile

./msToGlf -in msoutput -out msoutputNoInvar.gl -err 0.015 -depth 8 -nind 25 -singleOut 1