Generates an alternative reference sequence over the specified interval.
Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). Additionally, 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). Several important notes: 1) if there are multiple variants that start at a site, it chooses one of them randomly. 2) when there are overlapping indels (but with different start positions) only the first will be chosen. 3) this tool works only for SNPs and for simple indels (but not for things like complex substitutions). Reference bases for each interval will be output as a separate fasta sequence (named numerically in order).
The reference, requested intervals, and any number of variant rod files.
A fasta file representing the requested intervals.
java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T FastaAlternateReferenceMaker \ -o output.fasta \ -L input.intervals \ --variant input.vcf \ [--snpmask mask.vcf]
These Read Filters are automatically applied to the data by the Engine before processing by FastaAlternateReferenceMaker.
This tool uses a sliding window on the reference.
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).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--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)|
|--snpmask||RodBinding[VariantContext]||none||SNP mask VCF file|
|--variant||List[RodBinding[VariantContext]]||||variants to model|
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.
Maximum length of sequence to write per line.
An output file created by the walker. Will overwrite contents if file exists.
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.
SNP mask VCF file. Snps from this file are used as a mask when constructing the alternate reference. --snpmask binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3
variants to model. Variants from these input files are used by this tool to construct an alternate reference. --variant binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.