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MQ for non-variant positions
I need to filter both my variant and non-variant sites for calculation of window-based genetic diversity.
I am going to use the non-variant blocks in gvcf to filter the non-variant sites for coverage and genotype likelihood. However, I am filtering the variant sites also for MQ. To keep things comparable, I'd like to filter the non-variant sites for MQ as well, however, MQ is not reported in gvcf blocks.
Is there a way to get MQ for non-variant positions in gvcf? Or does MQ counted in the calculation of GQ for non-variant sites?