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New Varient Calling Tools/Consider GATK #37

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JasonJWilliamsNY opened this issue Aug 31, 2017 · 6 comments

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@JasonJWilliamsNY
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commented Aug 31, 2017

I know that newer versions of the tools we are using have deprecated some arguments we are using. Update? Also, now that GATK is going open, is it worth teaching this? I have never used it.

@crazyhottommy

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commented Aug 31, 2017

I was thinking why we are using bcftools to call SNVs. I have not used bcftools extensively. It is a genotyper caller the same as UnifiedGenotyper in GATK? for somatic mutations, I have used GATK (mutect1) recently, but it requires a lot of work to get a workable bam file: indel-realignment(mutect2 can skip this step but not stable yet), base quality recab etc... In a real world task with human genome, GATK is very slow, I have to parallelize every step by chromosome.

am working on a Snakemake pipeline on it for my own use: https://gitlab.com/tangming2005/snakemake_DNAseq_pipeline/tree/freebayes_anno

Best,
Tommy

@ErinBecker

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commented Oct 17, 2017

@JasonJWilliamsNY - Since we're preparing to release at the end of this month, I propose we hold off on any major content changes until our next release. Would love to have more discussion from the community on this issue to decide whether it's a good idea to make this change for then.

@tracykteal @fpsom @lexnederbragt @jrherr Any input?

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commented Oct 17, 2017

@tracykteal - This also sounds like a great question for the Genomics Curriculum Advisory Council. Can you please bring it to their attention?

@ErinBecker ErinBecker added the question label Oct 17, 2017

@crazyhottommy

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commented Oct 17, 2017

Let's hold it for our next release. it requires a lot of work to re-write this part.

@DCGenomics

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commented Nov 29, 2017

Perhaps we could reference genome in a bottle as a list of curated pipelines for variant calling: http://jimb.stanford.edu/giab/

ErinBecker pushed a commit that referenced this issue Feb 3, 2019

Merge pull request #37 from data-lessons/fpsom-patch-5
Updated config.yml based on the PR#128 of the canonical
@ErinBecker

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commented Mar 18, 2019

Thank you for all of the great discussion on this issue. With the recent integration of a newer variant calling tool in Feb 2019 (#133), I'm closing this issue. Please reopen if I've misread and there is more to resolve here.

@ErinBecker ErinBecker closed this Mar 18, 2019

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