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liggettla / FERMI

Fast Extremely Rare Mutation Identification
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Incorporate quality scores into base calling #63

Open liggettla opened 7 years ago

liggettla commented 7 years ago

Instead of using just cutoff frequencies like varThresh, what if quality scores could be incorporated into the collapsing to use actual probabilities to decide what the base in question actually is. By converting the fastq quality score to a phred score which represents actual probabilities of correct calls, this might be done.

https://github.com/GabePires/FastQ-Converter http://biopython.org/DIST/docs/api/Bio.SeqIO.QualityIO-module.html https://en.wikipedia.org/wiki/Phred_quality_score https://en.wikipedia.org/wiki/FASTQ_format

liggettla commented 7 years ago

Phred score can be calculated using the following:

python -c 'print ord("A")-33'

Or for the probability:

python -c 'from math import*; print 10**-((ord("A")-33)/10.0)'