CONTENTS:

1. R Files 
   a. pca - Statistical Analysis - VCF needs to be downloaded from 
      ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz
      and unzip 
      *packages need to be installed and functions sourced before getting output 
       by using pca <- PCA(read.vcfR('VCF file goes here') , read.csv('samples.csv'))
      
   b. HomoHeterozygosity - Population Analysis - Population diversity- VCF needs to be 
      downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz
      and unzip 
      *packages need to be installed and function sourced before getting output 
       by using HomoHeterozygosity(read.vcfR('VCF file goes here')); 2 outputs are 
       uploaded into global environment

   c. vst - Population Analysis - Vst - VCF needs to be downloaded from 
      ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz
      and unzip 
      *packages need to be installed, global variables need to be uploaded and functions sourced 
       before getting Vst data frames for each SV type by using DEL_Vst<-var_type_vst('DEL');
       DUP_Vst<-var_type_vst('DUP'); CNV_Vst<-var_type_vst('CNV')

   d. genes - Bioinformatic Analysis - program can be run either with test data from chromosome 1 
      or an entire dataset (3.b.) but CDS, UTR5 and UTR regions need to be downloaded 
      from http://genome.ucsc.edu/cgi-bin/hgTables
      *packages need to be installed, the entire or test datates need to be chosen (OPTION A/
       OPTION B) and functions sourced before getting an output data frame by using
       output <- findRegions(regions,UCSC_outputs)

2. BED Files
   a. gene_SYMBOL - Bioinformatic Analysis
   b. RVIS - Bioinformatic Analysis
   c. test_cds - Bioinformatic Analysis (OPTION A)
   d. test_utr5 - Bioinformatic Analysis (OPTION A)
   e. test_utr3 - Bioinformatic Analysis (OPTION A)

3. CSV Files
   a. samples - Statistical/ Population Analysis - contains all samples used in the structural
      variation discovery; ID, population, continental group and gender columns 

   b. NIHMS64772-supplement-Table_S6 - Bioinformatic Analysis - homozygous deletion regions
      used for dispensable gene discovery with entire dataset (OPTION B)

   c. test_regions - Bioinformatic Analysis - same as b. but only for chromosome 1; servs as 
      test data to run program without downloading CDS and UTR regions from UCSC Table Browser
      (OPTION A)

4. XLSX File 
   a. ID - IDs of structural variants stored in VCF which were used for analyses; 
      only informational purpose 