Return the entire VCF contents via picard?

biogreenbiogreen LondonMember

Hi
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?

Martin

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  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @biogreen
    Hi Martin,

    Thank you for sharing your solution.

    -Sheila

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