I am trying to find out how to identify if a snp is heterozygous or homozygous from the flags of a vcf file.
Maybe this is a trivial question but even if I read the vcf documentation I am still confused.
I am giving the following examples:
I have the following call from freebayes:
a) chr24 51 . C G 1458.24 . GT:DP:RO:QR:AO:QA:GL 1/1:50:0:0:50:1802:-5,-5,0
Based on a post that I read in SEQanswers by using the genotype likelihoods (PL tag in samtools vcf, GL in freebayes vcf) we have:
P(D|CC) = 10^(-5) = 0.00001
P(D|CG) = 10^(-5) = 0.00001
P(D|GG) = 10^(0) = 1
So, in that case can we say that the genotype is homozygous (GG) in my individual?
Can we say that in position 51 of the chromosome 24, the base in the reference sequence is C and the base in my individual is G which is homozygous?
chr24 55172 . G T 273.651 . GT:DP:RO:QR:AO:QA:GL 0/1:14:4:143:10:362:-5,0,-5
Here we have:
P(D|GG) = 10^(-5) = 0.00001
P(D|GT) = 10^(0) = 1
P(D|TT) = 10^(-5) = 0.00001
So, in that case can we say that the genotype is heterozygous (GT) in my individual?
And what exactly does it means?
Is that in position 55172 of the chromosome 24, the base in the reference sequence is G and the base in my individual is T but that T is heterozygous which is (G/T), or the REF and the ALT are the two zygotes of the SNP?
I am really sorry if my description is a little confusing.
Thank you very much in advance.