SURVIVOR merge is resulting in a lot of missing data, can I treat them as 0/0?

[qizhengyang2017]

My command is

SURVIVOR merge vcfs.txt 0.1 0 1 0 0 100 svim-asm_variants.vcf

Below are some lines of the SURVIVOR output which I changed format using bcftools. I wonder if I can treat the ./. as reference genotype?

CHROM	POS	ID	SVTYPE	SVLEN	CHR2	END	ARJ	AY	BAHC	BDR	BEL	CMiso	DHL92	DOYA	DUD	ESL	Harukei3	INB	KRY	NA	NUN	NY	OHG	PI161	PI164	PI414	PSR	QME	SAS	TOG	TVT	VEP
Cpichr01	21925	PI414.svim_asm.DEL.1	DEL	-319	Cpichr01	22244		1/1	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	1/1	1/1	./.	1/1	./.	./.	./.	./.
Cpichr01	29663	NA.svim_asm.DEL.1	DEL	-144	Cpichr01	29807		1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
Cpichr01	40685	PI414.svim_asm.INS.1	INS	252	Cpichr01	40685		1/1	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	1/1	./.	./.	./.	./.	./.	1/1	./.	1/1	./.	./.	./.	./.
Cpichr01	40702	INB.svim_asm.INS.1	INS	329	Cpichr01	40702		./.	./.	./.	1/1	./.	1/1	./.	./.	./.	./.	1/1	1/1	./.	./.	./.	1/1	./.	./.	./.	./.	1/1	./.	./.	./.	./.	1/1
Cpichr01	86520	INB.svim_asm.INS.2	INS	9342	Cpichr01	86520		./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	1/1	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.
Cpichr01	147143	VEP.svim_asm.INS.2	INS	3486	Cpichr01	147143		./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	1/1
Cpichr01	150014	KRY.svim_asm.INS.1	INS	380	Cpichr01	150014		1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1
Cpichr01	246939	INB.svim_asm.INS.4	INS	167	Cpichr01	246939		1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	./.	1/1	1/1	1/1	1/1
Cpichr01	246939	PI414.svim_asm.INS.3	INS	192	Cpichr01	246939		./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	1/1	./.	./.	./.	./.	./.	./.

[KrithikaSubramanian]

Hi,

I am also facing the same issue. It would be better if we could get a proper answer to this. Is ./. considered a reference genotype? Can we consider 0/0?

Thanks in advance,
Krithika S

[fritzsedlazeck]

Sorry for the slow reply ./. is undefined.. meaning that the SV was not in the input VCF file.
Hope that helps
Fritz