Difference of GT '1','1/1' in VCF file generated from isaac SNV calling

Hi guys,

I come across a issue in the VCF file generated from isaac SNV calling in illumina.

The GT contains "1" and "1/1". Do any one knows what's difference between them. Does "1" also means "homozygous"?

The GT = "1" are found in the chr 1, 2, besides chr x, y. (see the example below)

#CHROM  POS ID  REF ALT QUAL    FILTER  FORMAT  Sample A01
chr1    930751  rs3128111   C   G   153 PASS    GT:GQ:GQX:DP:DPF:AD 0/1:186:153:66:1:43,23
chr1    930892  rs2799059   T   C   87  PASS    GT:GQ:GQX:DP:DPF:AD 1:84:84:29:1:0,29
chr1    930923  rs2710882   A   G   541 PASS    GT:GQ:GQX:DP:DPF:AD 1/1:123:123:42:4:0,42

next-gen snp

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updated 3.9 years ago by Ram

• written 10.8 years ago by haoye.ecust •

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