1) QUAL (col 6) = Phred based score that the variant shown in the ALT col is wrong.
2) INFO (col 8) MQ flag = RMA mapping quality
The two scores do not have a linear relationship. Some variants have a high mapping quality, but lower QUAL....
Can anyone describe how these two scores are created and how they are related?
I want to be able to filter variants based on these two scores, but do not fully understand what they mean. Should i filter based on both scores or just 'QUAL' for variants?