Generate an alternative reference sequence over the specified interval
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).
The reference, requested intervals, and any number of variant ROD files.
A FASTA file representing the requested intervals.
java -jar GenomeAnalysisTK.jar \ -T FastaAlternateReferenceMaker \ -R reference.fasta \ -o output.fasta \ -L input.intervals \ -V 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.
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.
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 |
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
PrintStream stdout
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
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
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
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
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