Difference between WARP Exome Germline Single Sample and gatk4-exome-analysis-pipeline
Hello, what is the difference between the WARP and GATK4 exome pipelines?
In the online documentation on broadinstitute.github.io, it is stated that it is a Exome Germline Single Sample pipeline that implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data, which is what can be said about the gatk4-exome-analysis-pipeline as well.
What are the design differences and reasonings between the two, if there are any?
Thank you
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The WARP exome pipeline and gatk4-exome-analysis-pipeline are one and the same. Originally the pipeline was placed in GATK-Workflows Git Organization until the developers were able to establish a public Git repo of their own. The gatk4-exome-analysis-pipeline repo has now been archived and users are encouraged to use the latest version of the pipeline in the WARP repo.
Checkout this blog post for more background on WARP : Introducing-WARP-A-collection-of-cloud-optimized-workflows-for-biological-data-processing-and-analysis
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Beri,
when the announced DRAGEN pipeline with excluded BQSR comes out, will it replace the current WARP germline pipelines?
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According to the maintainers of the repo "there are planes to have it the replace the germline genome pipeline, it has not yet been tested on exomes, but would be after genomes are published. We will likely continue to maintain both versions for as long of a transition period is necessary. And of course old releases will always be available."
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Thank you Beri for the prompt response. So, in the transition period, will both workflows be considered GATK Best Practice?
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