Documentation

GATKPaperGenotyper

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

Category Toy Walkers (DevZone)

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.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

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).

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


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA