We are optimizing a custom pipeline that uses some of the functions from Samtools.1 and have a couple of questions about the parameters:
1) Coefficient for downgrading: This makes sense to us as a weighting coefficient that works on the quality scores, but we're a little confused by the formula. Is it correct to multiply the coefficient back to the INT or should it be a multiplier of the quality score (i.e., sqrt((INT-q)/INT)*q)?
From samtools.1 manual (http://samtools.sourceforge.net/samtools.shtml):
-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]
2) Where do the -i and -t parameters get implemented? And we’re not quite sure why setting them is important. Any information would be appreciated.
From samtools.1 manual (http://samtools.sourceforge.net/samtools.shtml):
-i FLOAT Ratio of INDEL-to-SNP mutation rate [0.15]
-t FLOAT Scaled mutation rate for variant calling [0.001]
THANKS!!
1) Coefficient for downgrading: This makes sense to us as a weighting coefficient that works on the quality scores, but we're a little confused by the formula. Is it correct to multiply the coefficient back to the INT or should it be a multiplier of the quality score (i.e., sqrt((INT-q)/INT)*q)?
From samtools.1 manual (http://samtools.sourceforge.net/samtools.shtml):
-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]
2) Where do the -i and -t parameters get implemented? And we’re not quite sure why setting them is important. Any information would be appreciated.
From samtools.1 manual (http://samtools.sourceforge.net/samtools.shtml):
-i FLOAT Ratio of INDEL-to-SNP mutation rate [0.15]
-t FLOAT Scaled mutation rate for variant calling [0.001]
THANKS!!
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