We have PacBio data where we want to do variant calling. I tried both UnifiedGenotyper and Haplotype caller. I was not very successfull doing that. When I used UnifiedGenotyper I got some output, but just SNPs but NO indels... (I skipped the realigment part there). I tried to play arround with the parameters (indelGapContinuationPenalty, indGapOpenPenalty, min_base_quality_score). Setting the "min_base_quality_score" to a lower value is giving at least this output with only SNPs as mentioned above.
The only manual for PacBio data on GATK I got was this: https://www.broadinstitute.org/gatk/guide/topic?name=methods
But this document is pretty old. Are there newer developments regarding GATK for PacBio? Or any more detailed tutorials?
Or would you suggest PBHoney as the right tool to use? Anything else?
Just to mention: For Illumina your toolkit worked like a charm! So basically we are able to work with it...
Thanks!
Michael