GATK best practice step-by-step command lines for Arabidopsis DNA-Seq data analysis
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
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Pierre Lindenbaum
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wangdp123
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wangdp123
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search the web for some pre-written workflows: here is an example with nextflow:
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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.