Resequencing using PacBio + using GATK HaplotypeCaller to call variants
We use the PacBio Blasr aligner for the alignment of our sequence constructs to the reference sequences.
Then, we use GATK HaplotypeCaller (default parameters) to call the variants (SNPs, Indels).
We're experiencing often the case that the HaplotypeCaller does not call variants although nicely highlighted by IGV (see screenshot attached).
Please, could anybody provide some helping hand?