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.
Depth
Depth
-doDepth 1 -doCount 1
Prints the frequencies of depths for each individual to .depth file.
Options
- maxDepth [int]
Defaults to 100. Sites with more than maxDepth reads are counted as having 100 reads.
Output
The outputfile .depth has one line per individual, with maxDepth entries.