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Quote from the samtools manual:
"-C 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. [0] "
I want to calculate how many reads are filtered by using -C50 -q30 in samtools mpileup, but I am not sure how the "phred-scaled probability q of being generated from the mapped position" was calculated in mpileup.
Does anyone know how this probability is calculated? Or does anyone know other ways to count/calculate filtered reads?
Thanks!
"-C 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. [0] "
I want to calculate how many reads are filtered by using -C50 -q30 in samtools mpileup, but I am not sure how the "phred-scaled probability q of being generated from the mapped position" was calculated in mpileup.
Does anyone know how this probability is calculated? Or does anyone know other ways to count/calculate filtered reads?
Thanks!