Genome Variant Analysis


java -jar GenomeAnalysisTK.jar -T ValidateVariants -R reference.fasta -V input.vcf --dbsnp dbsnp.vcf --reference_window_stop 208


Argument name(s)Default valueSummary
Required Inputs
NAInput VCF file
Optional Inputs
nonedbSNP file
Optional Parameters
[]which validation type to exclude from a full strict validation
Optional Flags
falseskip validation on filtered records
falseValidate this file as a GVCF
falsejust emit warnings on errors instead of terminating the run at the first instance

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