Learning-based parallel acceleration for HaplotypeCaller. #VariantCalling #HaplotypeCaller #GATK #Genomics #Bioinformatics #BMCbioinformatics 🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....

Release 4.6.0.0 · broadinstitute/gatk Download release: gatk-4.6.0.0.zip Docker image: https://hub.docker.com/r/broadinstitute/gatk/ Highlights of the 4.6.0.0 release: We've fixed a serious CRAM writing bug that affects GATK versions...

So 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.

#genomics #bioinformatics
github.com/broadinstitu...

This is a reply from #GATK on the recent ./. 0/0 blunder. Very interesting wording 😳 I think you can read a lot into it.

Why they didn't just fork the project for this purpose astounds me 🤷

At least it seems they have seen the light and might revert back and respect the VCF specifications 👍

This is from the #GATK post communicating that by default missing genotypes will be coded as 0/0 not the long-standing./.

I would hate to think what isn’t being communicated if this is a ‘banal’ change.
🧬🖥️

GenotypeGVCFs and the death of the dot If you have been keeping up with our GATK release notes, then you know that we have been rolling out a number of backend changes, tools, and features to GATK that we are hoping will improve the eff...

There has never been a clearer reason to use containerised version-controlled workflow managers such as #Nextflow. #GATK in some stroke of madness 🤪 will now code missing genotypes as 0/0 (DP = 0) instead of the long standing ./.
🧬🖥️

gatk.broadinstitute.org/hc/en-us/art...

Teaching genomics and snp calling with #gatk to @master_bcd students @ItropBioinfo @green_bioinfo