Understanding 1/1 output in VCF

Question

[LDT]

I have searched all around the internet, and it really bothers me that I do not get it.

Chromosome     position    REF   ALT    type 
  chr4          12345       A     A      0/0            / = unphased, | = phased
  chr5          43473       A     T      0/1 or 1/0
  chr6          34384       G    T,C     1/2            # multiallelic site with 2 alternative bases  
  chr7          74549       ?     ?      1/1

Could you help me understand what `1/11 means in the vcf output?

In here, it says: the sample is a homozygous alternate

In here. This basically means the base in the REF genome is the variant. and they give as an example for 1/1 the

To me, that looks like 0/1 or 1/0 type. Can someone explain me why this 1/1 and how on earth this related

1. The sample is a homozygous alternate --> there is no homozygosity
2. This basically means the base in the REF genome is the variant. ---> How on earth the base of the REF is the variant? What is the then the base on the sample?

[Pierre Lindenbaum]

Meaning Of Genotype 2/0 And 2/1 ; What Does Genetype ("0/0", "0/1" Or "1/1") In *.Vcf File Represent? ; ...

[4galaxy77]

"the sample is a homozygous alternate" is correct. "This basically means the base in the REF genome is the variant" this barely even makes sense to me, ignore it, especially since the website opens up a vcf in excel which you should never do.

[LDT]

Thank you for your comments. OK, I keep that the sample is homozygous to alternate. Could you then help me how the ? will be filled

  chrom       position    REF  ALT    type    
  chr7          74549      ?    ?      1/1

[Pierre Lindenbaum]

Could you then help me how the ? will be filled

? is not valid for the VCF format. The information is lost.

[LDT]

Yes yes, its a question mark, because I do not know how to fill it. Its. imposed by me and I am trying to find an example of what can be the REF and ALT in 1/1 case

[4galaxy77]

If you actually know what 1/1 means then it should be clear what you could put in the REF ALT column.

Answer 1

[karl.stamm]

The columns at left marked REF and ALT are not relevant to the subject/patient! It's important to think of a VCF containing possibly multiple samples in later columns to the right.

The left is a reference information, REF/ALT mean what are in the genome map and what isn't. The sample information being 1/1 means the sample is homozygous for the ALT and the REF is not found at all.

You could generate the VCF against a new genome reference with a different base at that point and the sample could become 0/0 because it's hom for the ref allele, "with respect to the genome used" and the REF/ALT column is only shown for convenience.

[LDT]

Thank you! I keep the …samples are homozygous for ALT and info im REF is not found I appreciate so much