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I am doing human exome sequencing with hg19 as a reference, and I want UnifiedGenotyper to give me whatever annotations are available and I will worry later about which ones are useful and which are not.
I am confused about the behavior of the --annotation option in UnifiedGenotyper. The default value is listed as , implying that unless we explicitly list what annotations we want, we get no annotations at all? Is that correct? Then in order to get a list of available annotations, we are directed to the VariantAnnotator --list option but it appears that it is not possible to just run:
java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T VariantAnnotator \ --list
In order to get a list of annotations. Instead, one not only needs to include a --variants flag, but the vcf file you point to actually has to be well-formatted, etc., otherwise you get errors like this
##### ERROR MESSAGE: Argument with name '--variant' (-V) is missing.
##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
So, that having failed, is anyone able to just provide me with a list of possible arguments to the UnifiedGenotyper --annotation option?