java -jar GenomeAnalysisTK.jar -T GenotypeConcordance -R reference.fasta -eval test_set.vcf -comp truth_set.vcf -o output.grp
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --comp | NA | The variants and genotypes to compare against | |
| --eval | NA | The variants and genotypes to evaluate | |
| Required Flags | |||
| --moltenize | false | Molten rather than tabular output | |
| Optional Outputs | |||
| --out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --genotypeFilterExpressionComp  -gfc | [] | One or more criteria to use to set COMP genotypes to no-call. These genotype-level filters are only applied to the COMP rod. | |
| --genotypeFilterExpressionEval  -gfe | [] | One or more criteria to use to set EVAL genotypes to no-call. These genotype-level filters are only applied to the EVAL rod. | |
| --printInterestingSites  -sites | NA | File to output the discordant sites and genotypes. | |
| Optional Flags | |||
| --ignoreFilters | false | Filters will be ignored | |