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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?

Thank you!

Best Answer


  • HomaHoma Member



    BP_RESOLUTION does not give MQ for non-variant sites. What I think I will use now is getting the callable/uncallable sites annotations with "Low mapping quality" so I can at least filter sites for mapping qualities in a more general way.


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