I am having an issue where the final merged output VCF file does not have the proper flag for whether the SNP was IMPUTED or TYPED. They are all correctly listed in the input info file and the individual input VCFs but then they all say IMPUTED for the final output VCF. I have tried this with the '--mixed_genotype_status' turned off (to output IMPUTED/TYPED based on the first input VCF) and with it turned on (to output ALL/SOME/NONE). Either way IMMERGE outputs that all SNPs were IMPUTED or NONE.
I am having an issue where the final merged output VCF file does not have the proper flag for whether the SNP was IMPUTED or TYPED. They are all correctly listed in the input info file and the individual input VCFs but then they all say IMPUTED for the final output VCF. I have tried this with the '--mixed_genotype_status' turned off (to output IMPUTED/TYPED based on the first input VCF) and with it turned on (to output ALL/SOME/NONE). Either way IMMERGE outputs that all SNPs were IMPUTED or NONE.