haplotypecaller doesn't emit genotype at all sites

beckyzhap

I've tried to get genotype for all sites provided in interval file using haplotypeCaller. If using unifiedGenotyper, I can get the result by setting "output_mode EMIT_ALL_SITES". But haplotypeCaller doesn't report as expected by "output_mode EMIT_ALL_SITES". Even though I set "genotypeFullActiveRegion" or "fullHaplotype", haplotypeCaller doesn't seem to emit genotype at all sites. How to get desirable result using haplotypeCaller? Thanks!

lucdh

Hi GATK team, Could it be this issue has not been resolved in GATK v 2.2.4? At least my recent attempts at getting HaplotypeCaller to report both variant and reference calls have failed, where UnifiedGenotyper with identical parameters works fine.

Geraldine_VdAuwera

This question has been asked and answered previously. Basically this cannot currently be done with HaplotypeCaller. We are working on it but we can't give you an ETA on when it will be possible.