ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
MsToGlf: Difference between revisions
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;-depthFile filename, This is useful if you want to force a different mean depth between individuals | ;-depthFile filename, This is useful if you want to force a different mean depth between individuals | ||
=Output format= | =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= | =Examples= | ||
Revision as of 21:58, 10 February 2014
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)'.