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
Jump to navigation
Jump to search
No edit summary |
|||
| Line 17: | Line 17: | ||
;-err errorrate, a value 0.005 corresponds to a 0.5% errorrate. | ;-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 | ;-depthFile filename, This is useful if you want to force a different mean depth between individuals | ||
=Output format= | |||
=Examples= | =Examples= | ||
Revision as of 21:54, 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