JEXL method to get the current sample name from single sample VCF file
I am experimenting with
JEXL expressions in order to do some hard filtering on variants. I wonder if there is a method to tell the filter expression to operate on the current sample (assuming here a single sample VCF file) without knowing the sample name a priori e.g.
Works just fine to sample heterozygous positions from a VCF where I know the sample will be called "Sample1", but can I refer to a sample name programmatically, e.g. something like:
vc.getGenotype( sample() ).isHet()
Sorry if this is a really dumb question. (BTW I realise you could use a
--genotypeFilterExpression "isHet == 1" to do the same thing, but I want to annotate the VCF in the
FORMAT/FILTER field, rather than the INFO field for downstream variant selection operations.