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remove private alleles from a vcf file

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

snp
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updated by Ram Ram • written by heinweb.teihnah • heinweb.teihnah

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

• 3 views • link
written by Katie D'Aco Katie D'Aco

2 answers

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


https://github.com/ekg/vcflib

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written by Zev.Kronenberg Zev.Kronenberg

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).

• 3 views • link
written by Adam Adam

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

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written by Katie D'Aco Katie D'Aco

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

• 0 views • link
written by jespinoz • jespinoz

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