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I would like to know how can I return the entire contents of a VCF file without having to know the chromosome/start/end parameters.
The VCFFileReader class has a query method that can return parts of the VCF like as:
VCFFileReader.query(chromosome, startPos, endPos);
What I would like is to be able to say: 'return everything the VCF has'.
Is there a way to do this with picard?