Emitting ref vs. alt allele counts on all sites

eranmick

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.

Geraldine_VdAuwera

If the sites aren't called as variants, those annotations will not be added by the UG. To do what you want, you would need to write a new annotation plugin for VariantAnnotator that counts alternate alleles.