Create an executable shell script that carries the data processing on vcf file (/data-shared/vcf_examples/luscinia_vars.vcf.gz). Count proportion of transitions (A -> G, G -> A, C -> T, T -> C) and transversions (A -> C/T, C -> A/G, G -> C/T, T -> A/G) in total and by type of nucleotide. Create .R script that prepares the graph visualising the results.
I made a shell script which analyzes /data-shared/vcf_examples/luscinia_vars.vcf.gz file and prints on standard output total number and proportion of transitions and transversion in total and also transitions and transversion for each nucleotide.
To run the solution clone this repository with
git clone https://github.com/CalounovaT/ngs-course-2020.git
Then move to this directory with
cd ngs-course-2020
To get the results run this command
./trans_script.sh
You should see the results printed
transitions = 206468 (0.61%)
transversions = 131944 (0.39%)
A -> C = 11758 (0.03%)
A -> G = 54261 (0.16%)
A -> T = 23421 (0.07%)
C -> A = 10824 (0.03%)
C -> G = 18966 (0.06%)
C -> T = 50124 (0.15%)
G -> A = 50969 (0.15%)
G -> C = 18091 (0.05%)
G -> T = 10951 (0.03%)
T -> A = 26219 (0.08%)
T -> C = 51114 (0.15%)
T -> G = 11714 (0.03%)
trans_script.sh also creates summary csv file in your home directory substitutions_results.csv with these results.
Then you can visualize the data with provided R script plot_script.R.
You can run the script with
Rscript plot_script.R
This will generate file Rplots.pdf in your home directory containing the plots.
Alternatively you can view them in Rstudio.
