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Values for indel qualities

I am a researcher from the Politecnico di Milano.
I would like to ask a clarification about the indel qualities transition probabilites of the PairHMM in HaplotypeCaller.

I am using some of your tutorial data (specifically NA12878_wgs_20.bam) and I have noticed that insertion and deletion qualities are always equal, is this always the case?

Moreover, all the reads seem to share these characteristics:

  • the last base has always an indel quality of 45, why?
  • the other bases have indel qualities of 40 or increasingly lower depending on the surrounding context (under four repetitions the indel quality is 40, for eight repetitions the indel quality is 39 and so on). Are you using an affine gap model with open penalty (-5) and continuation penalty (-1)?

Thanks for considering my request.


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