Pierre LindenbaumI asked #biostars : "Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the system., exiting."
https://www.biostars.org/p/9614740/
#bioinformatics #parabricks #NVIDIA #haplotypecaller #gatk #gpus
Ben FultonKnow what would have been cool? If Broad hadn't broken two thirds of the links in the GATK documentation when they redid the website.
https://xcancel.com/gatk_dev/status/1908902547521257779 "GATK Dev Team :" GATK forums will be community-driven and self-moderated. They will not be moderated or monitored by a GATK team member. We encourage members of the community to continue to engage with each other on these forums." https://gatk.broadinstitute.org/hc/en-us/community/topics
TIL: You can get a list of Spark-enabled GATK tools with the command
gatk --list | grep Spark
(The website doesn't seem to have a list anywhere)
#gatk dependencies graph : https://deps.dev/maven/org.broadinstitute%3Agatk/4.6.1.0/dependencies/graph
https://github.com/nf-core/modules/pull/6619 PR accepted for nf-core/modules/gatk/VariantsToTable #gatk 🥳
Luke PembletonSo after much community backlash #GATK has reverted back to the ./. representation for no-calls.
The question is, will something like this occur again? and how many people have already switched away to other tools like #bcftools.
I know I have moved all my pipelines back to bcftools and honestly its brilliant.
https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot "GenotypeGVCFs and the death of the dot" #gatk
@thatdnaguy You prompted me to properly look it this, so I ran some tests to empirically test when GATK deviated away from #VCF specifications, rather than rely on the unclear changelogs. All the results and datasets are up on my GitHub repo 🧬🧮
https://github.com/lpembleton/gatk4-when-did-dot-leave
TL;DR: missing data representation with ”./.” ceased to exist in #GATK version 4.2.3.0. If you want to retain correct VCF specification and “./.” stick with version 4.2.2.0 or earlier 👍
GitHub - lpembleton/gatk4-when-did-dot-leave: Confirmation of which GATK4 versions go against VCF specifications and call missing GT as 0/0 instead of ./.
Confirmation of which GATK4 versions go against VCF specifications and call missing GT as 0/0 instead of ./. - lpembleton/gatk4-when-did-dot-leave
CellBioNewsAnalytic tool rapidly reveals #genetic #diversity for next-generation #crop breeding.
#agriculture #snp #GATK #HPC_GVCW
https://phys.org/news/2024-03-analytic-tool-rapidly-reveals-genetic.html
