Question: -C 50 parameter MPILEUP
4 weeks ago by
f1978hp • 0
f1978hp • 0 wrote:
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?
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