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Deletion tends to have lower indel quality than insertion
Hi the Team,
I am analyzing some small target PCR-based deep sequencing data. The target region is 264067 bp, median of interval average coverage is around 5000x. I did indel realignment and base quality recalibration in preprocess. After BQSR, I found that for almost all reads, the BI quality (round 55) is higher than BD quality (round 45).
In the following variants calling step, we found much more deletions than insertions.
May I know that it is a normal behavior for the data having higher BI quality than BD quality?