What is the best practice to prepare input bam files for calling RNA editing ?

[YibiChen]

Base on what I read in the manual, only filtering for uniquely mapped reads and marking PCR duplicates are recommended.

However, in a stardard SNP analysis, which is very similar to the RNA editing analysis, people would do local realignment around the indel, Base Quality Score Recalibration and Variant Quality Score Recalibration.

Do you see the benefit of doing these corrections? If so, how would them affect the filtering criteria in JACUSA2?