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 applies the following downsampling settings by default.
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 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|
|NA||Input VCF file|
||none||SNP mask VCF file|
|stdout||An output file created by the walker. Will overwrite contents if file exists|
|60||Maximum length of sequence to write per line|
|NA||If specified, heterozygous SNP sites will be output using IUPAC ambiguity codes given the genotypes for this sample|
|false||Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity)|
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
int 60 [ [ -? ? ] ]
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 (inserting N's in the sequence) when constructing the alternate reference (regardless of whether they overlap a variant site).
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.
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).
GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA