I have no idea if someone has made a galaxy pipeline to do this. The general steps are as follows:
- Sort and index the BAM file (this can be done with samtools)
- Use samtools mpileup like in this post: Questions Regarding Consensus Sequence Calling With Samtools / Bcftools / Vcfutils.Pl Note that I think you can skip the bcftools part step and just give samtools mpileup the -v option.
You can use the bam2cns module of proovread (https://github.com/BioInf-Wuerzburg/proovread). It is a consensus based PacBio-Illumina correction software. An advantage might be that the module let's you set a coverage cutoff and it only considers the best alignments (by score) for each location up this cutoff. This is paricularly useful, if you are dealing with repetitive regions, where suboptimal alignments introduce a lot of noise.