meaning of genotype

Question

[arwa.ahmad95]

Hello

I want to ask a question: when I look to vcf file I found this number in genotype (GT): 0/2, 1/2, 2/2, 0/3, 1/3,2/3,3/3,0/4,1/4,2/4,3/4, 4/4, 0/5,1/5,2/5,3/5,4/5,5/5,0/6,1/6,2/6,3/6,4/6,5/6,6/6 I didn't underatand the meaning of the number can any one explain the meaning of this genotype

[Pierre Lindenbaum]

Meaning Of Genotype 2/0 And 2/1

[arwa.ahmad95]

I didn't see before 6 ALTs . I have 2 queations here: 1- what is the maximum ALT ? 2- how can I know the number of ALT in my vcf? ( when I open using note is appear like just Alt only )

Answer 1

[Pierre Lindenbaum]

what is the maximum ALT ?

in the htslib api, the number of alleles is 2^16: https://github.com/samtools/htslib/blob/develop/htslib/vcf.h#L221

uint32_t n_info:16, n_allele:16;

how can I know the number of ALT in my vcf? (

 awk -F '\t' '/^[^#]/ {N=split($5,a,/[,]/);printf("%s:%s:%s %d\n",$1,$2,$4,N);}' in.vcf

[arwa.ahmad95]

Thank you very much. The last question : as 0/0 is homo so for example 5/5 is homo ? and 1/6 is hetro?