haplotypecaller doesn't emit genotype at all sites

beckyzhapbeckyzhap Posts: 2Member
edited October 2012 in Ask the GATK team

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!

Post edited by Geraldine_VdAuwera on

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