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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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. | 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. | ;Sorry about the total lack of information for this program. | ||
This program assumes diploid samples. | |||
=Brief Overview= | =Brief Overview= | ||
<pre> | <pre> | ||
Revision as of 21:53, 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