do Hisat2 and STAR mappers use a Bayesian algorithm to map reads over the genome?
STAR's algorithm is described in the publication.
One for HISAT2 is probably in its publication (I can't see the paper in full at this time).
No. These tools use discrete algorithms to find and score the alignments for the reads. HISAT genotype implements an inference algorithm to help determine the abundance of alleles and mappings over them, but STAR and HISAT1/2 don't.
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