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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Emitting ref vs. alt allele counts on all sites

Hi,

I would like to use UnifiedGenotyper to produce a vcf file where all sites I specify via BED file will have a count of reads carrying the reference allele and a count of reads carrying an alternate allele, regardless of whether a variant has been called in the site.
I've tried to use EMIT_ALL_SITES, but this appears not to provide this count breakdown for sites that are not called as variable.
I would appreciate any pointers. I am using GATK 2.2.4.

Thank you very much.

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