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Unified Genotyper: VCF files where genotype is not called

mike_boursnellmike_boursnell Posts: 69Member

Hi. I have run UnifiedGenotyper and the output VCF file has :

When the genotype is called you get: GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 (i.e. five colon-separated fields as expected)

When the genotype is not called you get: GT:AD:DP:GQ:PL ./.:.:1 (i.e. only three colon-separated fields)

Version: (version 2.7-1-g42d771f)

Is this a bug or is this expected?

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