This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Can anyone share me a good GATK4 workflow

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
• 5,867 views • link
written by Ambu Vijayan • Ambu Vijayan

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

• 0 views • link
written by Jeremy Leipzig Jeremy Leipzig

I am actually trying to run it and then by practise learn what everything does.

• 0 views • link
written by Ambu Vijayan • Ambu Vijayan

5 answers

Completly, agree - there's a real lack of clarity when it comes to documentation of some tools and options. And it's only trolling through dozens of forum posts on any number of issues that you can begin to troubleshoot common issues. Example workflows won't resolve those headaches but the following resources may help you get started.

  1. IBM White Paper - I found this most useful because I didn't want a .wdl cromwell workflow. https://www.ibm.com/downloads/cas/ZJQD0QAL
  2. NIH HPC has a Good GATK4 tutorial/workflow with detailed explanations and examples I wish had been available when I made my workflow - https://hpc.nih.gov/training/gatk_tutorial/
  3. Broad github .wdl scripts - Not ideal if you don't want to use .wdl, but they can still clarify some things. Making them even less ideal, the Broad regularly deems these scripts as 'outdated'. https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels and also https://github.com/gatk-workflows/gatk4-basic-joint-genotyping/blob/main/gatk4-basic-joint-genotyping.wdl
  4. Workflow using Nextflow for the variant calling - https://github.com/gencorefacility/variant-calling-pipeline-gatk4
• 0 views • link
written by Marsha • Marsha

Thank you so much for these, I will look into it and let you know.

• 0 views • link
written by Ambu Vijayan • Ambu Vijayan

If you're looking for a streamlined yet comprehensive explanation of GATK4 and the main Best Practices workflows, you may be interested in the O'Reilly book I co-authored called Genomics in the Cloud. (The cloud part is secondary, all the GATK-focused explanations are applicable pretty much regardless of where you will run the workflows).

See https://oreil.ly/genomics-cloud

• 0 views • link
written by vdauwera vdauwera

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.

• 0 views • link
written by dr_cfoster dr_cfoster

I tried that but so much is explained without any context.

• 0 views • link
written by Ambu Vijayan • Ambu Vijayan

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.

• 0 views • link
written by cpad0112 cpad0112

Just to add to the growing list. Here is a Snakemake workflow I created to call germline mutations using GATKs best practice guidelines. Maybe it helps you.

https://github.com/nickhir/GermlineMutationCalling

Cheers!

• 0 views • link
written by nhaus • nhaus

Log in to answer this question.

More posts like this