Mills reference for indel VQSR
Posted in Ask the GATK team | Last updated on


Comments (6)

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?


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