vcf-merge and vcftools –relatedness

Just wanted to get some stuff regarding VCF-merge down before I forgot how I did it. Notebooks are important huh?

This will largely be psedu-code, as I’m writing it on a computer separate from the files, but should be easly transferable/extendable.

This assumes that all vcf files are located in a common directory, I may extend it to crawl through a series of directories, but that seems excessive at the moment.

vcf.filenames<- list.files(path = "directory", pattern = ".vcf")
## Goes through and bgzips and tabixs each file, a requirement of vcf-merge
for(i in 1:leng(vcf.filenames))   {
  
  system("bgzip -c ", vcf.filenames[i])
  system("tabix -p ", vcf.filenames[i], ".gz")
  
}

## performes the actual merge on all avaialble bgzipped files. It would be wise to only have VCF files in this directory, so strange things don't happen.
system("vcf-merge *.gz > merged.vcf")

system("vcftools --relatedness --vcf merged.vcf --out relatedness")

Just tested this on a subset of files and it worked, so that’s one step closer to actually running MACAU!