Variant Call Format - Explanation Of Quality Scores?

Question

[Ian]

In variant call format (VCF) files produced at the end of the samtools mpileup variant detection pipeline there are two quality scores:

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?

Thanks.

Answer 1

[Jeremy Leipzig]

mapping quality is assigned by the aligner and are wildly different from aligner to aligner. It is like e-val but less useful. Every aligner will assign a different mapping quality based on what it internally estimates the probability is that a read is accurately placed.

If you start filtering based on mapping quality you run the risk of biasing against SNPs that are in repeats or gene families.

[Jeremy Leipzig]

yes, this is called MAPQ in SAM and is arguably the least popular column

[Ian]

Just to clarify - you are talking about MQ, right? Thanks for replying, i couldn't find anything as useful on the VCF site (unless i missed it...).