Vcf-Stats

Question

[alok.helix]

Can somebody explain to me what does private in vcf stats mean??

hom_AA_count' => 4299, 'het_RA_count' => 458, 'snp_count' => 4757, 'count' => 9977, 'hom_RR_count' => 5220, 'ref' => 5678, 'missing' => 16, 'private' => 134, 'snp' => {

Answer 1

[Ashutosh Pandey]

Assuming 'private' here refers to private variants. Private variants are those variants that are not found in other samples or are unique to a given sample in a multiple sample VCF file. For example, If my variant file or VCF file consists of 5 different strains of mice. There will be lot of variants that are exclusive to a strain and not present in other strains. In this case, those variants will be counted as private for that strain.

[alok.helix]

Thank you bhai!!So bhaiya, can you explain the difference between between true singleton and private doubleton??