Best alignment tool for PacBio data

[gevro]

Hi,
What is the recommended aligner for Pacbio data before running DeepVariant? bwa? pbmm2?
Thanks.

[AndrewCarroll]

Hi @gevro,

Early in building the PacBio models, we benchmarked on both NGMLR and Minimap2/pbmm2 and found that they gave similar quality of variant calls. We train with data from Minimap2/pbmm2, and I would recommend using pbmm2 for the mapper.