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#gatk — Public Fediverse posts

Live and recent posts from across the Fediverse tagged #gatk, aggregated by home.social.

  1. 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.

    gitlab.univ-nantes.fr/pierre.l

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

  2. 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.

    gitlab.univ-nantes.fr/pierre.l

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

  3. github.com/WeTheAgents/markdup
    "
    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

  4. github.com/WeTheAgents/markdup
    "
    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

  5. 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

  6. 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

  7. xcancel.com/gatk_dev/status/19 "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." gatk.broadinstitute.org/hc/en-

    #gatk

  8. xcancel.com/gatk_dev/status/19 "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." gatk.broadinstitute.org/hc/en-

    #gatk

  9. 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

  10. 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

    github.com/broadinstitute/gatk

  11. 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

    github.com/broadinstitute/gatk

  12. @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 🧬🧮

    github.com/lpembleton/gatk4-wh

    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

  13. @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 🧬🧮

    github.com/lpembleton/gatk4-wh

    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

  14. 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

  15. 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

  16. 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. 🙄

  17. 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. 🙄

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

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

  20. #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? 🤷

    gatk.broadinstitute.org/hc/en-

    #bioinformatics #genomics

  21. #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? 🤷

    gatk.broadinstitute.org/hc/en-

    #bioinformatics #genomics

  22. 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

  23. 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

  24. 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-

  25. 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-

  26. 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. ( gatk.broadinstitute.org/hc/en- )

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

    #sam #bam #bwa

  27. 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. ( gatk.broadinstitute.org/hc/en- )

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

    #sam #bam #bwa

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

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

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

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

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

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

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

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