Question: What is the diffeernce between singletons and doubletons - VCFtools
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gravatar for haneenih7
6 months ago by
haneenih760
haneenih760 wrote:

Hi all,

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 :)

population genetics snp • 405 views
ADD COMMENTlink modified 5 months ago • written 6 months ago by haneenih760
1
gravatar for haneenih7
5 months ago by
haneenih760
haneenih760 wrote:

--singletons option in VCFtools produces a file contains singletons and doubletons. Singletons are SNPs that only show up once in a single individual, and that individual is heterozygotic for that allele (genotype (0/1). On the other hand, doubletonsare SNPs also show up once in one individual but that individual is homozygotic for the allele (genotype 1/1)

ADD COMMENTlink modified 5 months ago • written 5 months ago by haneenih760
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