Select minimum set of SNPs from VCF file to identify a individual
I have a VCF file containing SNP information for over 1000 samples. I have preprocessed the original VCF file using VCFtools with filters --max-alleles 2, --minDP 20, --minQ 30, and --maf 0.3, Hardy-Weinberg equilibrium, linkage disequilibrium.
Now, I want to identify a minimal set of informative SNPs that, if genotyped, can be used to determine the probable origin of a DNA sample. Please suggest a program to perform this task. I do not have any experience in coding.
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