SEQanswers Samtools.1 Parameter Q's
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 09-15-2011, 09:48 AM #1 msleslie Junior Member   Location: San Diego Join Date: Sep 2011 Posts: 1 Samtools.1 Parameter Q's 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!!
09-15-2011, 10:03 AM   #2
rskr
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Location: Santa Fe, NM

Join Date: Oct 2010
Posts: 250

Quote:
 Originally Posted by msleslie 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!!
This is interesting. In the benchmarking I have done the mapping qualities haven't been so relevant, because they haven't correlated well with accuracy of the alignments, maybe there is a better way to calculate them.

 Tags parameters, pipeline development, samtools, samtools consensus