Haplotype-based resolution of variants in separate callsets.
HaplotypeResolver is a tool that takes two 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.
Two variant files to resolve.
A single consensus VCF.
java -jar GenomeAnalysisTK.jar \ -T HaplotypeResolver \ -R reference.fasta \ -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.
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 Outputs | |||
| --out -o |
stdout | File to which variants should be written | |
| Optional Parameters | |||
| --setKey |
set | Key used in the INFO key=value tag emitted describing which set the combined VCF record came from | |
| --statusKey |
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
VariantContextWriter stdout
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.
String set
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.
String status
Input VCF file
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
R List[RodBinding[VariantContext]] NA