Entering edit mode
2.1 years ago
yoser4
▴
10
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 ^-^
/
: genotype unphased|
: genotype phased.
allele is missingHelloļ¼Asaf .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.
As a matter of fact - Biostars is all you need What Are Phased And Unphased Genotypes?