Why are measured base insertion and deletion qualities only Q45 for BaseRecalibrator?

trgalltrgall Posts: 13Member

The measured qualities of the BI and BD are 45 in for this library. Normally I have a wide range for I and D qualities from 39-61. I have tried setting -ddq and -idq to -1, but that doesn't change anything. I am using dbsnp137 for my knowns, and otherwise just use default settings.

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output2.pdf
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  • CarneiroCarneiro Posts: 274Administrator, GATK Dev admin

    Looks like you're missing the POST RECALIBRATION plots in this PDF. It is only showing the original qualities, which for I/D are defaulted to Q45 since Illumina doesn't provide error estimates from the instrument.

  • trgalltrgall Posts: 13Member

    I'm not sure what you mean "POST RECALIBRATION".

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