Dear, I perform the snp detection with Varscan on several genotypes. And now I tried to combine all vcf files in order to construct one matrix : genotype x snp. For each snp: If is found call the snp, if not, call the reference allele.

bcftools isec --collapse all --output-type v -p genotype1.vcf genotype2.vcf genotype3.vcf --output matrix.txt

Is it the good way ? Thanks a lot !