FastaReferenceMaker

Create a subset of a FASTA reference sequence

Category Reference Utilities

Traversal LocusWalker

PartitionBy LOCUS


Overview

This tool creates a new reference in FASTA format consisting of only those positions or intervals provided in the input data set. 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. Each interval has a description line starting with a greater-than (">") symbol followed by sequence data. The description begins with the contig name followed by the beginning position on the contig.

 For example, the fasta file for contig 1 and intervals 1:3-1:4 and 1:6-1:9
 >1 1:3
 AT
 >1 1:6
 GGGG
 

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T FastaReferenceMaker \
   -R reference.fasta \
   -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.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

Command-line Arguments

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

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
stdout 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
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

Maximum length of sequence to write per line

int  60  [ [ -∞  ∞ ] ]


--out / -o

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

PrintStream  stdout


--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  false


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GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.