Looking for MQ for non-variants, unsure why MMQ given as 0 for them.
I'm doing quality control on outputs, both variant and non-variant, and I was hoping to have mapping quality for non-variants as well as variants but they are not given. I have produced my file using HaplotypeCaller and then produced a vcf from that file using GenotypeGVCFs with the parameter -ERC GVCF. I tried using BP_RESOLUTION but non-variants still did not possess MQ scores. In addition I am unclear as to why the MMQ is 0 for all non-variants as I did not change the minimum mapping quality score from 10 in the previous steps which I understand to be the default.