Hi everyone! I have 3 vcf files that I have to merge into one single vcf and then convert to binary bed format using plink, because I need to run a paternity test. I have all my files in a directory in HPC, in which all the softwares that I would need (like GATK or Plink and then King for relatedness inference) are already installed.
Let's say that I have 3 vcf files: proband.vcf.gz, mother.vcf.gz, father.vcf.gz. First of all, should I gunzip them? Now, I don't have anything else in my directory other than these 3 files. What are the steps to merge them into one and then convert them? Do I need other files that I have to download to do this?
This is the only command that I'm sure of, after merging the vcfs.
plink --vcf file.vcf --biallelic-only strict --double-id --vcf-filter --make-bed --out outfile
Thank you in advance.