GATK

Tagged with #all sites
0 documentation articles | 0 events or announcements | 1 forum discussion

Sorry, there are no publicly available documents of this type with the tag #all sites. Try one of the other types.
Sorry, there are no publicly available documents of this type with the tag #all sites. Try one of the other types.

haplotypecaller doesn't emit genotype at all sites

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!