FastaReferenceMaker

Renders a new reference in FASTA format consisting of only those loci provided in the input data set.

Category Reference Utilities

Traversal LocusWalker

PartitionBy LOCUS

Overview

The output format can be partially controlled using the provided command-line arguments. Specify intervals with the usual -L argument to output only the reference bases within your intervals. Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a separate fasta sequence (named numerically in order).

Input

The reference and requested intervals.

Output

A fasta file representing the requested intervals.

Examples

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T FastaReferenceMaker \
   -o output.fasta \
   -L input.intervals

Additional Information

Read filters

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

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

FastaReferenceMaker 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
--lineWidth	int	60	Maximum length of sequence to write per line
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists
--rawOnelineSeq	boolean	false	Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity)

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.

--lineWidth / -lw ( int with default value 60 )

Maximum length of sequence to write per line.

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

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

--rawOnelineSeq / -raw ( boolean with default value false )

Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity). Please note that when using this argument adjacent intervals will automatically be merged.

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