Haplotype-based resolution of variants in 2 different eval files.
HaplotypeResolver is a tool that takes 2 VCF files and constructs haplotypes based on the variants inside them. From that, it can resolve potential differences in variant calls that are inherently the same (or similar) variants. Records are annotated with the set and status attributes.
2 variant files to resolve.
A single consensus VCF.
java -Xmx1g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T HaplotypeResolver \ -V:v1 input1.vcf \ -V:v2 input2.vcf \ -o output.vcf
These Read Filters are automatically applied to the data by the Engine before processing by HaplotypeResolver.
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.
|--variant||List[RodBinding[VariantContext]]||NA||Input VCF file|
|--out||VariantContextWriter||stdout||File to which variants should be written|
|--setKey||String||set||Key used in the INFO key=value tag emitted describing which set the combined VCF record came from|
|--statusKey||String||status||Key used in the INFO key=value tag emitted describing the extent to which records match|
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.
File to which variants should be written.
Key used in the INFO key=value tag emitted describing which set the combined VCF record came from. Set to 'null' if you don't want the set field emitted.
Key used in the INFO key=value tag emitted describing the extent to which records match. Set to 'null' if you don't want the status field emitted.
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.