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

ADD COMMENTlinkeditmoderate 9 months ago wangdp123 • 150 • updated 9 months ago Pierre Lindenbaum 120k
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Have you checked the GATK presentations? https://software.broadinstitute.org/gatk/documentation/presentations

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

ADD REPLYlinkeditmoderate 9 months ago
igor
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search the web for some pre-written workflows: here is an example with nextflow:

https://github.com/oliverSI/GATK4_Best_Practice

ADD COMMENTlinkeditmoderate 9 months ago Pierre Lindenbaum 120k

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