Can anyone share me a good GATK4 workflow
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9 weeks ago

Can anyone share me a good GATK4 workflow, I Couldnt find anything good that explanins the process in a crisp and easy way.

gatk gatk4 • 201 views
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is your goal to run it or understand it? ideally both I'm sure but in reality these may be somewhat opposing goals

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9 weeks ago
cfos4698 ▴ 270

I don't think you'd find many better resources for GATK4 than those provided by the Broad Institute themselves. Check out the getting started page and the best practices described within.

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9 weeks ago

There are several example scripts online for GATK pipeline. May not be the best, crisp and easy way. Here is GATK workflow for variant calling in RNAseq (https://ssvbio.github.io/rna-seq-and-gatk-best-practices). Probably applicable for WGS and WES for human samples.

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