remove private alleles from a vcf file

Question

[heinweb.teihnah]

Hello

is there an inbuild way to remove singletons from a vcf file? I would just really need to use vcf tools to just exclude them from the vcf file and than recode it into a new vcf file without the singleton variants.

The problem is that --singletons only uses the positions fo the singletons

[Katie D'Aco]

Could you use the output of --singletons as an input file for vcftools --positions option?

Answer 1

[Zev.Kronenberg]

vcflib has a tool called vcffilter that can be used to do what you are asking.

https://github.com/ekg/vcflib

Answer 2

[Adam]

In vcftools, you could just use a small MAF to achieve this. Something like --maf 0.0001 would achieve what you need (assuming you have fewer than 5000 samples).

[Katie D'Aco]

Clever solution, although this would miss any "private doubletons" in the dataset.

[jespinoz]

Is MAF minimum or maximum allele frequency and what would I set it at for 88 samples?