How to read vcf files

Question

[yoser4]

Hello, I have a vcf file. In the GT field, I am not very clear about some statements, which mainly include eight types:

.|.
./.
0|0
0/0
0|1
0/1
1|1
1/1

What I know is(Help from GATK official website):

- 0/0 : the sample is homozygous reference
- 0/1 : the sample is heterozygous, carrying 1 copy of each of the REF and ALT alleles
- 1/1 : the sample is homozygous alternate

I want to know what the following types mean (about the difference between "|" and "/"):

.|.
./.
0|0
0|1
1|1

Any help will be appreciated ^-^

[Asaf]

/ : genotype unphased

| : genotype phased

. allele is missing

[yoser4]

Hello，Asaf .thanks for your help. My understanding is that 0/0 represents ref/ref, 0/1 represents ref/alt, and 1/1 represents alt/alt. I don't know if my understanding is correct. I'm a novice in bioinformatics. I don't know what you mean by "unphased" and "phased". Can you elaborate on "|" and "/". Or is there a detailed website that I can read.

[Asaf]

As a matter of fact - Biostars is all you need What Are Phased And Unphased Genotypes?

Answer 1

[Asaf]

A duplicate of: What Are Phased And Unphased Genotypes?

[yoser4]

Can I understand that 0/1 represents Aa, while 0 | 1 may represent Aa or aA. I can roughly think that the variations of 0/1 and 0 | 1 are consistent. Is that correct?

[Asaf]

The opposite - 0/1 represents wither Aa or aA while 0|1 represents Aa.

[yoser4]

thank you veeeeeeeeery much !