FastaAlternateReferenceMaker

Generate an alternative reference sequence over the specified interval

Category Reference Utilities

Traversal LocusWalker

PartitionBy LOCUS


Overview

Given a variant callset, this tool replaces the reference bases at variation sites with the bases supplied in the corresponding callset records. Additionally, it allows for one or more "snpmask" VCFs to set overlapping bases to 'N'.

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).

Caveats

  • If there are multiple variants that start at a site, it chooses one of them randomly.
  • When there are overlapping indels (but with different start positions) only the first will be chosen.
  • This tool works only for SNPs and for simple indels (but not for things like complex substitutions).

Input

The reference, requested intervals, and any number of variant ROD files.

Output

A FASTA file representing the requested intervals.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T FastaAlternateReferenceMaker \
   -R reference.fasta \
   -o output.fasta \
   -L input.intervals \
   -V input.vcf \
   [--snpmask mask.vcf]
 

Additional Information

Read filters

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

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

Window size

This tool uses a sliding window on the reference.

  • Window start: -1 bp before the locus
  • Window stop: 50 bp after the locus

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.

FastaAlternateReferenceMaker 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
Required Inputs
--variant
 -V
NA Input VCF file
Optional Inputs
--snpmask
none SNP mask VCF file
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
--use_IUPAC_sample
 -IUPAC
NA If specified, heterozygous SNP sites will be output using IUPAC ambiguity codes given the genotypes for this sample
Optional Flags
--rawOnelineSeq
 -raw
false Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity)
--snpmaskPriority
false SNP mask priority

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


--snpmask / -snpmask

SNP mask VCF file
SNPs from this file are used as a mask (inserting N's in the sequence) when constructing the alternate reference

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3

RodBinding[VariantContext]  none


--snpmaskPriority / -snpmaskPriority

SNP mask priority
Gives priority to a SNP mask over an input VCF for a site. Only has an effect if the --snpmask argument is used.

Boolean  false


--use_IUPAC_sample / -IUPAC

If specified, heterozygous SNP sites will be output using IUPAC ambiguity codes given the genotypes for this sample
This option will generate an error if the specified sample does not exist in the VCF. Non-diploid (or non-called) genotypes are ignored.

String  NA


--variant / -V

Input VCF file
Variants from this VCF file are used by this tool as input. The file must at least contain the standard VCF header lines, but can be empty (i.e., no variants are contained in the file).

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3

R RodBinding[VariantContext]  NA


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