GATK best practice step-by-step command lines for Arabidopsis DNA-Seq data analysis

Question

[wangdp123]

Hi there,

I am interested in using GATK best practice to call SNP/InDels for DNA-Seq samples from Arabidopsis populations. But I am struggling to find out the step-by-step command lines for such kind of analysis. Which pipeline would you command?

Could you please direct me to the correct website that I can find the detailed specific command lines with arguments for each step?

Many thanks,

Tom

[igor]

Have you checked the GATK presentations? https://software.broadinstitute.org/gatk/documentation/presentations

The various workshop contain detailed instructions and examples for each step.

Answer 1

[Pierre Lindenbaum]

search the web for some pre-written workflows: here is an example with nextflow:

https://github.com/oliverSI/GATK4_Best_Practice