java -jar GenomeAnalysisTK.jar -R reference.fasta -T VariantAnnotator -I input.bam -V input.vcf -o output.vcf -A Coverage -L input.vcf --dbsnp dbsnp.vcf
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--variant  -V | NA | Input VCF file | |
Optional Inputs | |||
--comp | [] | Comparison VCF file | |
--dbsnp  -D | none | dbSNP file | |
--resource | [] | External resource VCF file | |
--snpEffFile | none | SnpEff file from which to get annotations | |
Optional Outputs | |||
--out  -o | stdout | File to which variants should be written | |
Optional Parameters | |||
--annotation  -A | [] | One or more specific annotations to apply to variant calls | |
--excludeAnnotation  -XA | [] | One or more specific annotations to exclude | |
--expression  -E | {} | One or more specific expressions to apply to variant calls | |
--group  -G | [] | One or more classes/groups of annotations to apply to variant calls | |
--MendelViolationGenotypeQualityThreshold  -mvq | 0.0 | GQ threshold for annotating MV ratio | |
Optional Flags | |||
--alwaysAppendDbsnpId | false | Add dbSNP ID even if one is already present | |
--list  -ls | false | List the available annotations and exit | |
--resourceAlleleConcordance  -rac | false | Check for allele concordances when using an external resource VCF file | |
--useAllAnnotations  -all | false | Use all possible annotations (not for the faint of heart) |