UnifiedGenotyper supports --output_mode EMIT_ALL_SITES (default EMIT_VARIANTS_ONLY). Will HaplotypeCaller have a similar option in the future?
HaplotypeCaller used to have that option, but it was removed when we introduced the reference model (gVCF) option. Have a look at the documentation that explains this here: http://www.broadinstitute.org/gatk/guide/article?id=2940
Gerladine, thank you for answering my question and pointing me to gVCF. According to the documentation it currently only works for single sample calling. I like UG --output_mode, because it can be combined with for example --alleles GENOTYPE_GIVEN_ALLELES. This is useful when doing "single population calling" and merging those VCF files after variant calling with CombineVariants. Thanks again.
That makes sense. Unfortunately we're sort of sitting in between two chairs right now with HaplotypeCaller; we're working on complementary features to enable this functionality in the context of multi-sample/population studies, but in the meantime we had to deactivate the emit-all function. Sorry for the inconvenience!