Adjusting prior using external indel predictions and confidence calculations

[a113n]

It's me again :) I am personally very interested in your work and STR variations in general, so I hope you don't mind me asking more about the details of your algorithm.

In your paper, you suggested that indels from tools like Samtools, Dindel etc can be used to adjust the prior distribution of repeat length. I might have overlooked but it seems like you are only adjusting fragment length instead of adjusting the prior.

//line 535-550 of japsa/src/main/java/japsa/bio/tr/Fragment2TRV.java        
                if (indel !=null && refIndexIndel == fragment.getReferenceIndex()){
                    Indel eIndel = indel;
                    int eIdx = indelIdx;
                    while (eIndel.chr.equals(indel.chr) && eIndel.start < fragment.getEnd()){
                        fragment.iSize += eIndel.length;
                        eIdx ++;
                        if (eIdx < indelList.size()) 
                            eIndel = indelList.get(eIdx);
                        else 
                            break;
                    }
                }


                double v = fragment.getISize();

If I have a list of indels predicted from GATK haplotypecaller, and I want to use that to adjust the prior of STRviper calls, how could I best achieve that?

My second question is related to the confidence calculation. I noticed that quality score of the STRviper VCF are low in general (most are below 20), so I want to learn how that was calculated in the paper but to no avail. I looked at the source code and found the relevant code in line 643 of japsa/src/main/java/japsa/bio/tr/Fragment2TRV.java.

trv.setConfidence(d.cumulativeProbability(trv.getVar() - 0.5, trv.getVar() + 0.5));

I don't quite understand why +- 0.5 was chosen as the threshold to calculate the confidence. Could you point me to the rationale behind that? Thank you very much!

Cheers,
Allen