I am interested in calling errors (especially indels) in my PacBio alignments. I want ALL errors to be reported, not only high frequency ones. Thus, the best for me would an alternative to mpileup for Illumina reads. I am considering two options here:
1) using PacBio-specific software, something along the lines of:
variantCaller.py --algorithm=quiver chr22_P6.cmp.h5 -r hg19.fa -o variants.gff -o consensus.fasta -o consensus.fastq
2) Tweaking mpileup by turning of all the probabilistic realignments, something along the lines of:
samtools mpileup sam/forward/chr21_P6.cmp.h5.bam.forward.bam -f reference.fa -l feature.bed -uv --no-BAQ --open-prob 15 -Q 0 -D -t INFO/DPR
I have both .cmp.h5 and bam files with alignments.