remove private alleles from a vcf file
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7.4 years ago

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 • 3.3k views
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Could you use the output of --singletons as an input file for vcftools --positions option?

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7.4 years ago

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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7.4 years ago
Adam ★ 1.0k

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).

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

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

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