#gatk — Public Fediverse posts

ugly, but it works: I can run a maximum of 50 jobs with a maximum of 500 cpus on our server.

So I run 10 # gatk HaplotypeCaller in parallel in one nextflow process using `make -j 10` ===> 500 gatk HC at the same time.

https://gitlab.univ-nantes.fr/pierre.lindenbaum/gazoduc-nf/-/blob/master/modules/gatk/hapcaller2/main.nf?ref_type=heads#L81

#nextflow #gatk #make #makefile #bioinformatics #workflow

ugly, but it works: I can run a maximum of 50 jobs with a maximum of 500 cpus on our server.

So I run 10 # gatk HaplotypeCaller in parallel in one nextflow process using `make -j 10` ===> 500 gatk HC at the same time.

https://gitlab.univ-nantes.fr/pierre.lindenbaum/gazoduc-nf/-/blob/master/modules/gatk/hapcaller2/main.nf?ref_type=heads#L81

#nextflow #gatk #make #makefile #bioinformatics #workflow

https://github.com/WeTheAgents/markdup8x-wea
"
markdup-wea: Rust rewrite of Picard MarkDuplicates — 3.26x faster, 54x less RAM, byte-identical output on 8 ENCODE RNA-seq samples vs Picard 3.4.0. Plus nf-core/rnaseq Picard memory-tuning proposal"

#bioinformatics #gatk #rust

https://github.com/WeTheAgents/markdup8x-wea
"
markdup-wea: Rust rewrite of Picard MarkDuplicates — 3.26x faster, 54x less RAM, byte-identical output on 8 ENCODE RNA-seq samples vs Picard 3.4.0. Plus nf-core/rnaseq Picard memory-tuning proposal"

#bioinformatics #gatk #rust

I 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

I 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

I 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

I 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

I 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

Know what would have been cool? If Broad hadn't broken two thirds of the links in the GATK documentation when they redid the website.

#BroadInstitute #GATK

Know what would have been cool? If Broad hadn't broken two thirds of the links in the GATK documentation when they redid the website.

#BroadInstitute #GATK

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

#gatk

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

#gatk

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)

#bioinformatics #GATK #ApacheSpark

#gatk dependencies graph : https://deps.dev/maven/org.broadinstitute%3Agatk/4.6.1.0/dependencies/graph

#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 🥳

https://github.com/nf-core/modules/pull/6619 PR accepted for nf-core/modules/gatk/VariantsToTable #gatk 🥳

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.

I know I have moved all my pipelines back to bcftools and honestly its brilliant.

#genomics #bioinformatics

https://github.com/broadinstitute/gatk/releases/tag/4.6.0.0

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.

I know I have moved all my pipelines back to bcftools and honestly its brilliant.

#genomics #bioinformatics

https://github.com/broadinstitute/gatk/releases/tag/4.6.0.0

https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot "GenotypeGVCFs and the death of the dot" #gatk

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 👍

#genomics #bioinformatics

@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 👍

#genomics #bioinformatics

Analytic 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

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

Why they didn’t fork the project for this purpose rather then continue on the main branch astounds me 🤷

At least it seems they have seen the light and might revert back and respect the VCF specifications.
#bioinformatics #genomics

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

Why they didn’t fork the project for this purpose rather then continue on the main branch astounds me 🤷

At least it seems they have seen the light and might revert back and respect the VCF specifications.
#bioinformatics #genomics

The thing about #GATK switching from observing the VCF specification to not isn't that I'm surprised they made the change. They can do what they want with their software.
It was my ignoring that it was going to happen. The mountain of previous experience show that the changes they introduce are poorly documented in their own community, forget the wider community. In the last several months I had to create a GATK docker image. It's an older version. Because subconsciously I didn't trust newer. 🙄

The thing about #GATK switching from observing the VCF specification to not isn't that I'm surprised they made the change. They can do what they want with their software.
It was my ignoring that it was going to happen. The mountain of previous experience show that the changes they introduce are poorly documented in their own community, forget the wider community. In the last several months I had to create a GATK docker image. It's an older version. Because subconsciously I didn't trust newer. 🙄

@lwpembleton is that the fault of the #gatk developers or those that use tools without testing them for suitability 🤔

@lwpembleton is that the fault of the #gatk developers or those that use tools without testing them for suitability 🤔

#GATK v4.2.3.0 which violates VCF specifications and calls missing genotypes as 0/0 instead of ./. was released in 2021, and they have only just now written a blog post about it 🤯 @!$# describing it as a 'feature'.

How many papers published since then now have potential errors in them due to downstream analyses that look for ./. as a missing genotype call? 🤷

https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot

#bioinformatics #genomics

#GATK v4.2.3.0 which violates VCF specifications and calls missing genotypes as 0/0 instead of ./. was released in 2021, and they have only just now written a blog post about it 🤯 @!$# describing it as a 'feature'.

How many papers published since then now have potential errors in them due to downstream analyses that look for ./. as a missing genotype call? 🤷

https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot

#bioinformatics #genomics

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. #Bioinformatics

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. #Bioinformatics

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 ./.

https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot

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 ./.

https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot

I was given a BAM. I see the following tags in the SAM:

'de:f:0.0067 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:288'

#GATK HaplotypeCaller crashed because of those tags. ( https://gatk.broadinstitute.org/hc/en-us/community/posts/11440622639387-Unable-to-trim-uncertain-bases-without-flow-order-information )

The only tools used (header/@PG) are bwa: 7.15-r1142-dirty and MarkDuplicates.
which tool added those tags ?

#sam #bam #bwa

I was given a BAM. I see the following tags in the SAM:

'de:f:0.0067 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:288'

#GATK HaplotypeCaller crashed because of those tags. ( https://gatk.broadinstitute.org/hc/en-us/community/posts/11440622639387-Unable-to-trim-uncertain-bases-without-flow-order-information )

The only tools used (header/@PG) are bwa: 7.15-r1142-dirty and MarkDuplicates.
which tool added those tags ?

#sam #bam #bwa

#gatk 4.4.0.0 released: https://github.com/broadinstitute/gatk/releases/tag/4.4.0.0 moved to #Java 17

#bioinformatics

#gatk 4.4.0.0 released: https://github.com/broadinstitute/gatk/releases/tag/4.4.0.0 moved to #Java 17

#bioinformatics

https://www.nature.com/articles/s41598-022-26181-3 "Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment" #gatk #dragen #deepvariant #genomics #wgs

https://www.nature.com/articles/s41598-022-26181-3 "Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment" #gatk #dragen #deepvariant #genomics #wgs

https://www.nature.com/articles/s41598-022-26181-3 "Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment" #gatk #dragen #deepvariant #genomics #wgs

https://www.nature.com/articles/s41598-022-26181-3 "Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment" #gatk #dragen #deepvariant #genomics #wgs

I got a new bug in #gatk : https://github.com/broadinstitute/gatk/issues/8106

I've have the feeling that the #VCF called by ILMN / #dragen and #gatk are quite different. 🤔

I've have the feeling that the #VCF called by ILMN / #dragen and #gatk are quite different. 🤔

I've have the feeling that the #VCF called by ILMN / #dragen and #gatk are quite different. 🤔

I've have the feeling that the #VCF called by ILMN / #dragen and #gatk are quite different. 🤔