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# FastaReferenceMaker

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

## 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


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

### 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).

### FastaReferenceMaker 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
NA An output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--lineWidth
-lw
60 Maximum length of sequence to write per line
Optional Flags
--rawOnelineSeq
-raw
NA 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

Maximum length of sequence to write per line

int  [ [ -∞  ∞ ] ]

### --out / -o

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

PrintStream

### --rawOnelineSeq / -raw

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.

boolean