java -jar GenomeAnalysisTK.jar -T ValidateVariants -R reference.fasta -V input.vcf --dbsnp dbsnp.vcf
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --variant  -V | NA | Input VCF file | |
| Optional Inputs | |||
| --dbsnp  -D | none | dbSNP file | |
| Optional Parameters | |||
| --validationTypeToExclude  -Xtype | [] | which validation type to exclude from a full strict validation | |
| Optional Flags | |||
| --doNotValidateFilteredRecords | false | skip validation on filtered records | |
| --validateGVCF Â -gvcf | false | Validate this file as a GVCF | |
| --warnOnErrors | false | just emit warnings on errors instead of terminating the run at the first instance | |