If I run HaplotypeCaller with a VCF file as the intervals file, -stand_emit_conf 0, and -out_mode EMIT_ALL_SITES, should I get back an output VCF with all the sites from the input VCF, whether or not there was a variant call there? If not, is there a way to force output even if the calls are 0/0 or ./. for everyone in the cohort?
I have been trying to run HC with the above options, but I can't understand why some variants are included in my output file and others aren't. Some positions are output with no alternate allele and GTs of 0 for everyone. However, other positions that I know have coverage are not output at all.
I would like to trigger calls at HapMap sites even if they are HOM_REF in my sample. I used to accomplish this in an older GATK version with the following parameter passed to the UnifiedGenotyper: -B:trigger,VCF hapmap.vcf Right now I am using version 1.6 of the GATK. How could I accomplish exactly the same with this new version?
What I am trying to do (when doing VariantEval on the detected SNPs) is to obtain GenotypeConcordance for all: HETs, HOM_REFs, and HOM_VAR. Currently I only get the concordance values for HETs and HOM_VAR on the VariantEval output. Asked in a different way, how could I get the 'n_true_HOM_REF_called_*' fields populated in the VariantEval?
Thanks for your help, Gene