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Step-by-step command lines for plant DNA-Seq data analysis

wangdp123wangdp123 United KingdomMember

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?

Many thanks,

Dapeng

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