#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

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

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

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

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

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'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. 🤔