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Interpretaiton of VCF file format for GT section

nikkinathnikkinath GermanyMember
edited March 2016 in Ask the GATK team

Dear all,

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



  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    The 1/2 genotype simply means the genotype contains the first alternate allele and the second alternate allele. The reference allele is 0, the first alternate allele is 1, the second alternate allele is 2...and so on.

    Have a look at the VCF spec under "1.4.2 Genotype fields" for more information.


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