I am using GATK 188.8.131.52 to perform somatic variant calling with Mutect2. I obtained the final (single-sample) VCF file(s) and annotated it with Funcotator, and would now like to convert it into a table with the fields of interest for the analysis I am planning to do.
Everything works fine, but I am encountering some issues with the 'FUNCOTATION' INFO field. This field comprises dozens of "sub-fields", delimited by pipes ( | ) (e.g. Gencode_28_hugoSymbol | Gencode_28_ncbiBuild | Gencode_28_chromosome | etc etc).
Using "-F FUNCOTATION" correctly adds the FUNCOTATION column to the resulting table. What I would like to do, though, is extracting specific "sub-fields" from the FUNCOTATION field and add the corresponding columns to the table. From what I had gathered from the user guide, I was expecting "-ASF FUNCOTATION" to separate FUNCOTATION into distinct fields itself, and to enable the usage of "-F" to extract the desired ones (e.g. "-ASF FUNCOTATION -F Gencode_28_hugoSymbol"). However, this doesn't seem to be working, and the only effect of "-ASF FUNCOTATION" seems to be removing the square brackets from the FUNCOTATION field column in the final table, leaving it as a non-divisible entity.
Am I doing something wrong, or is the "FUNCOTATION" field not divisible in its 'sub-fields' in any way?
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