This is a repo for all the scripts written by myself used in the final project of BIOS26120 Fall 2017 at UChicago
This is used to count the number of variants in .vcf file on each chromosome.
This reads in the output of the first script and plot the distribution of variants on chromosomes in a pie chart.
This plots the quality distribution of all the genotyped variants, which led to the identification of HQ220 and HQ30 sets in my report.
This does most of the functional analyses the output of ANNOVAR in HQ220 set.
This analysis the distribution of variants in three-letter codons, to varify that snynonymous mutations are more frequent at the third position.
The source code for typeset the final report.