#gatk — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #gatk, aggregated by home.social.
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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.
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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.
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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
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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
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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
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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
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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
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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)
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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.
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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.
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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 ? -
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 ? -
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
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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
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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
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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
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