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

[JHitz]

I am also wondering about this. I found something similar in chr1. My called genotype is "1/.". The depth is good so I'm not sure why this would ever been called for chr1-22?

[haoye.ecust]

"1" represents a haploid call, such as on the non-PAR regions of X and Y for a male sample. RTG Core variant callers also automatically output haploid or diploid calls as appropriate for the region and sex of the sample being processed.

Thanks very much, Len. However, I just checked the results. I found the '1' is also occurs on chr 1, 2, not only in chr X, Y (see following). PS, the SNVs are called from a WGS illumina Hiseq2000 with coverage ~80X.

#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

[Len Trigg]

"1" represents a haploid call, such as on the non-PAR regions of X and Y for a male sample. RTG Core variant callers also automatically output haploid or diploid calls as appropriate for the region and sex of the sample being processed.

[haoye.ecust]

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"?

Thanks