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## Bug Report
### Affected tool(s) or class(es)
N/A
### Affected version(s)
- [ x] Latest public release version [4.5.0.0]
- [ ] Latest master branch as of [date of test?]
### Description …
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@fnothaft has concerns (upon which he will elaborate) regarding the testing process.
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And benchmark expected performance changes
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This almost-working code can replace remote tabix, but there are a few issues:
1. Downstream scripts expect empty format fields to be present (as ".") but GATK removes them
2. duplicate records ar…
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I have migrated gatk to arm architecture, but the running speed is too slow, so I want to use GKL. Can I build GKL on ARM architecture? Could you help me?
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## Bug Report
### Affected tool(s) or class(es)
"gatk PostprocessGermlineCNVCalls"
### Affected version(s)
- docker (broadinstitute/gatk, 4.1.9.0 version)
### Description
#### Steps to re…
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https://github.com/tgen/phoenix/blob/9f04da2fdcce834e152158cf437ba7be8a9969d3/modules/constitutional/gatk_genotypegvcf.jst#L112-L152
Test run to determine if this can detect a block subsitution pro…
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An Rmarkdown report, similar to what we have for alignment and other pipelines.
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### Instructions
gatk --java-options "-Xmx256g -XX:ParallelGCThreads=10" GenotypeGVCFs -R ./Zm_Mo17.fa -stand-call-conf 0 -ploidy 1 -V gendb:///share/home/gaochenxu/01.prj/50.pan-maize/2.sv/pan/03…
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Hi, thank you so much for the great tool.
I'm trying to apply longshot on long-read RNA-seq data (Iso-seq data from PacBio HiFi reads).
I ran the pipeline with default options and got ~30% reads …