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Quick Start

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conkline edited this page Mar 23, 2018 · 9 revisions

assessPool Quick Start

  1. To run assessPool, you will need: Rstudio, samtools, cpan, vcftools v0.1.12 or higher, vcflib, and (optionally) GNU parallel
  2. Navigate to desired working directory on your computer
  3. Clone repo into directory: git clone https://github.com/ToBoDev/assessPool.git
  4. Open assessPool Rproject in RStudio
  5. Open assessPool_main.Rmd file in RStudio
  6. Make sure you have your SNP file (.vcf) and reference file (.fasta) in the working directory
  7. Note - the first time you run the script, library installation (via packrat) will take some time.
  8. Follow the steps in the main file to complete your analysis - run each code chunk and adjust parameters as needed

Software (c) E Freel, E Conklin, D Kraft, J Whitney 2018; Manual by E Conklin

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