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.