As my question in SO was closed and asked to be posted in this forum, I am posting it here.
I am not from the bioinformatics domain. However, for the sake of analysis, I am trying to pick up certain basics related to the GT field in the VCF file.
I know we have a field called
Alleles. May I know under what circumstances GT takes a certain value and how they are called? Can you confirm my understanding?
Ref Alt GT Name A A 0/0 Homozygous A G 0/1 Heterozygous (does 1/0 also mean the same?) What's this 0 and 1 actually? A [C,CA] ?? ?? ?? ?? 1/1 HOM_ALT? How and why?
Can the experts here help me to fill the
question marks and also help me understand with the Ref and Alt combinations when a genotype can take a value of 0/0 or 1/0 or 1/1 or 1/2 etc. and what are the names for those values? Like when it is called HOM_ALT etc.?
Any simple explanation for beginner like me (with no background in bioinformatics/biology) can be helpful.