Showing docs for version 3.6-0 | The latest version is 4.1.4.0


GATKPaperGenotyper

Simple Bayesian genotyper used in the original GATK paper

Category Variant Discovery Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

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.


Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by GATKPaperGenotyper.

Parallelism options

This tool can be run in multi-threaded mode using this option.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

Command-line Arguments

Engine arguments

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.

GATKPaperGenotyper specific arguments

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

Argument details

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.


--log_odds_score / -LOD

The LOD threshold for us to call confidently a genotype

double  3.0  [ [ -∞  ∞ ] ]


--out / -o

An output file created by the walker. Will overwrite contents if file exists

PrintStream  stdout


Return to top


See also GATK Documentation Index | Tool Docs Index | Support Forum

GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.