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Interpretaiton of VCF file format for GT section
After running Haplotyper caller, I get a VCF file. To understand the vcf file, I am following this document http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it.
According to GT section, in the output there should be one option among the following
0/0 - the sample is homozygous reference 0/1 - the sample is heterozygous, carrying 1 copy of each of the REF and ALT alleles 1/1 - the sample is homozygous alternate
However, in my output vcf file we also find values like GT 1/2, I am not sure how to interpret this output.
Could you please suggest what does this mean? I am using Haplotyper caller to call the variants