I've used vcftools ( --singletons option) to identify singletons in my vcf file. I want to know what is the difference between singletons and doubletons. I am very confused after what I read in the VCFtools manual that the:
--singletons option will generate a file detailing the location of singletons, and the individual they occur in. The file reports both true singletons, and private doubletons (i.e. SNPs where the minor allele only occurs in a single individual and that individual is homozygotic for that allele).
I know that singletons are SNPs only show up once in a single individual. On the other hand, doubleton is an allele occurs twice in one individual. However, based on the VCFtools manual, doubletons mean SNPs only occurs in a single individual and that individual is homozygotic for that allele
Does this mean that a singleton is an allele occurs only once, and that individual is heterozygotic for that allele? (opposite than doubletons)?
And what does private doubleton mean?
Thank you :)