GATKPaperGenotyper

A simple Bayesian genotyper, that outputs a text based call format.

Category Variant Discovery Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

Intended to be used only as an example in the GATK publication.

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.

TreeReducible (-nt)

Command-line Arguments

Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

CommandLineGATK

GATKPaperGenotyper specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Optional
--log_odds_score	double	3.0	The LOD threshold for us to call confidently a genotype
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists

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 ( double with default value 3.0 )

The LOD threshold for us to call confidently a genotype.

--out / -o ( PrintStream with default value stdout )

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

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.