kaichop
commented
2 years ago The GT of 0/0 means that there is no mutation at this site in this individual. It is reference genotype.
On Wed, Dec 29, 2021 at 9:51 PM qing @.***> wrote:
Dear Prof. Wang,
I'm sorry for interrupting you. I am using ANNOVAR to annotate my vcf file. When I used convert2annovar.pl to convert vcf file into an avinput file, I found a problem. All my variants that GT is 0/0 directly removed. I saw a sentence in the ANNOVAR Documentation is ' The input contains seven loci, but many of them do not have non-reference genotypes for the first sample' , but I don’t quite understand why the sites that GT is 0/0 is non-reference genotypes. I have just been exposed to genome analysis, and the basic knowledge is still lacking. Looking forward to your reply!
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>
Dear Prof. Wang,
I'm sorry for interrupting you. I am using ANNOVAR to annotate my vcf file. When I used convert2annovar.pl to convert vcf file into an avinput file, I found a problem. All my variants that GT is 0/0 directly removed. I saw a sentence in the ANNOVAR Documentation is ' The input contains seven loci, but many of them do not have non-reference genotypes for the first sample' , but I don’t quite understand why the sites that GT is 0/0 is non-reference genotypes. I have just been exposed to genome analysis, and the basic knowledge is still lacking. Looking forward to your reply!