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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
Variant calling of PacBio data using UnifiedGenotyper or HaplotypeCaller
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...