Haplotype-based resolution of variants in separate callsets.
java -jar GenomeAnalysisTK.jar -T HaplotypeResolver -R reference.fasta -V:v1 input1.vcf -V:v2 input2.vcf -o output.vcf
| 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 | |