Simple Bayesian genotyper used in the original GATK paper
This is a very simple implementation of a Bayesian genotyper that outputs a text based call format. It was developed solely to serve as a toy example in the original GATK publication, and should NOT be used in actual analysis work.
These Read Filters are automatically applied to the data by the Engine before processing by GATKPaperGenotyper.
This tool can be run in multi-threaded mode using this option.
This tool applies the following downsampling settings by default.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Outputs | |||
| --out -o |
stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --log_odds_score -LOD |
3.0 | The LOD threshold for us to call confidently a genotype | |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
The LOD threshold for us to call confidently a genotype
double 3.0 [ [ -∞ ∞ ] ]
An output file created by the walker. Will overwrite contents if file exists
PrintStream stdout