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Hi all --
This should be a simple problem -- I cannot find a valid version of the Mills indel reference in the resource bundle, or anywhere else online!
All versions of the reference VCF are stripped of genotypes and do not contain a FORMAT column or any additional annotations.
I am accessing the Broad's public FTP, and none of the Mills VCF files in bundle folders 2.5 or 2.8 contain a full VCF. I understand that there are "sites only" VCF, but I can't seem to find anything else.
Can anyone link me to a version that contains the recommended annotations for indel VQSR, or that can be annotated?