FastaStats

Calculate basic statistics about the reference sequence itself

Overview

These are very basic statistics: total number of bases and number of "regular" bases (i.e. A, C, T or G).

Input

A FASTA reference file.

Output

Base counts are written to file if an output file name is given (with -o), otherwise output to stdout.

Example

 java -Xmx2g -jar GenomeAnalysisTK.jar \
-T FastaStats \
-R ref.fasta \
[-o output.txt]


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

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).

FastaStats 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

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.

--out / -o

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

PrintStream  stdout

GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA