-C 50 parameter MPILEUP

Question

[f1978hp]

In Samtools documentation are this descrition:

-C, --adjust-MQ INT     

Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50.

Why downgrading mapping quality? And, why 50 is a value recommended for BWA?

Thanks,

FM

[finswimmer]

Hello,

using this parameter bcftools penalize read with lot of mismatches harder than most aligner will do, which greatly improve specificity in variant calling. The thought behind this, is to say the more mismatches in one read exists the higher the probability that the origin of this read is in another region.

Why 50 for bwa? I guess the authors of bcftools just try it out :) According to the given formular the value must be higher than 40. Because bwa's mapping quality goes up to the value. If C is set lower you might get a negative value below the sqrt which is not allowed.

If you have region with high variability -C 50 might be to strict. I often use -C 60.

fin swimmer