I'm trying to find the way to call variants for a PacBio library. All the reads come from a similar construct (~1300 bp) on which we introduced several random mutations, each mutation set is associated with a particular barcode, for this reason, I have demultiplexed my reads applying a custom script over the circular consensus sequence, so now I want to get the mutational set associated with the barcodes.
I have been searching for ways to call the variants for PacBio Reads, but I have run into problems with some of the tools. For example, I aligned my demultiplexed reads with blastr and then I saved the output in xml format, but when attempted to use quiver it returns "Parse error" that seems to be related with the xml. I tried also running quiver with a bam file but this also returned an invalid "PacBio BAM file" error, I think quiver needs the cmp.h5 file, but I don't have that file and I also don't know if that could be useful to the kind of information that I want to get.
I've tried MICADo but for that algorithm, I have a problem running the example data set that they provide.
I also read that using GATK for long reads would not be ideal.
Is there any other tools that work with xml/bam/sam/fastq files from PacBio which could be useful for my plasmid library?