Can anyone share me a good GATK4 workflow

Question

[Ambu Vijayan]

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

[Jeremy Leipzig]

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

[Ambu Vijayan]

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

[Ambu Vijayan]

I will look into it. Thank you.

Answer 1

[Marsha]

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 Making them even less ideal, the Broad regularly deems these scripts as 'outdated'.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

[Ambu Vijayan]

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

Answer 2

[vdauwera]

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

[Ambu Vijayan]

Thank you so much

Answer 3

[cfos4698]

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.

[Ambu Vijayan]

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

Answer 4

[cpad0112]

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.

Answer 5

[nhaus]

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!