Hi Sheila and Geraldine
When I run HaplotypeCaller (v3.3-0-g37228af) in GENOTYPE_GIVEN_ALLELES mode with --emitRefConfidence GVCF I get the error:
Invalid command line: Argument ERC/gt_mode has a bad value: you cannot request reference confidence output and GENOTYPE_GIVEN_ALLELES at the same time
It is however strange that GENOTYPE_GIVEN_ALLELES is mentioned in the --max_alternate_alleles section of the GenotypeGVCFs documentation.
Maybe I'm missing something?
Thanks,
Gerrit
