loading VCF file

library(vcfR)

## 
##    *****       ***   vcfR   ***       *****
##    This is vcfR 1.13.0 
##      browseVignettes('vcfR') # Documentation
##      citation('vcfR') # Citation
##    *****       *****      *****       *****

getwd()

## [1] "/Users/omchauhan/Documents"

list.files(pattern = "vcf")

## [1] "9.36073098-36313098.ALL.chr9_GRCh38.genotypes.20170504.vcf"   
## [2] "9.36073098-36313098.ALL.chr9_GRCh38.genotypes.20170504.vcf.gz"
## [3] "all_loci.vcf"                                                 
## [4] "ALL.chr9_GRCh38.genotypes.20170504.vcf.gz"                    
## [5] "code_checkpoint_vcfR.html"                                    
## [6] "code_checkpoint_vcfR.rmd"                                     
## [7] "vcfR_test.vcf"                                                
## [8] "vcfR_test.vcf.gz"

my_snps <- vcfR::read.vcfR("9.36073098-36313098.ALL.chr9_GRCh38.genotypes.20170504.vcf", convertNA = T)

## Scanning file to determine attributes.
## File attributes:
##   meta lines: 130
##   header_line: 131
##   variant count: 6984
##   column count: 2513
## 
Meta line 130 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
##   Character matrix gt rows: 6984
##   Character matrix gt cols: 2513
##   skip: 0
##   nrows: 6984
##   row_num: 0
## 
Processed variant 1000
Processed variant 2000
Processed variant 3000
Processed variant 4000
Processed variant 5000
Processed variant 6000
Processed variant: 6984
## All variants processed