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

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 • 1.2k views
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