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Quick Start
conkline edited this page Mar 23, 2018
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- To run assessPool, you will need: Rstudio, samtools, cpan, vcftools v0.1.12 or higher, vcflib, and (optionally) GNU parallel
- Navigate to desired working directory on your computer
- Clone repo into directory:
git clone https://github.com/ToBoDev/assessPool.git - Open assessPool Rproject in RStudio
- Open assessPool_main.Rmd file in RStudio
- Make sure you have your SNP file (.vcf) and reference file (.fasta) in the working directory
- Note - the first time you run the script, library installation (via packrat) will take some time.
- 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