genotype field in vcf file
In SNP analysis, the result file in vcf file format, would have a field of genotype of the strains analysed. The genotype 0/0 means both the alleles are that of the reference genome. But then how is it an SNP if both alleles match the reference genome? Can anybody explain it to me, please?
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duplicate: How to interpret reference homozygous genotype in the VCF file generated by GATK
show us a line of your vcf and explain us how it was generated.