Why remove multiallelic sites ?
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9 weeks ago

Hello, I have some questions about this filter.I work with WES so :

vcftolls --min-alleles 2 --max-alleles 2 --recode --out
  1. I understand that it is used to maintain only biallelic sites, but what is the reason for maintaining only these types of variants? Is it because multi-allelic variants are rare and you are more likely to be able to get a false positive call? Or is it because from the analysis of the child population it is better to have 2 alleles in ref and in alternative changes?

  2. I applied this filter and it doesn't remove anything. The variants keep the same set, why? Is the fact that I don't have multi-allelic sites in my set available?

Thank you, I appreciate all your clarifications.

sites multiallelic • 377 views
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vcftolls -> vcftools. vcftools is deprecated. use bcftools.

but what is the reason for maintaining only these types of variants? I

the answers depends of the analysis you're doing

Is it because multi-allelic variants are rare

they're not. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288273/

In a deep sequencing study, 10% of the variant site can be multi-allelic.

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Hi thanks, i was so confused , the reason that i mention to be rare is by this blog thanks https://gatk.broadinstitute.org/hc/en-us/articles/360035890771-Biallelic-vs-Multiallelic-sites

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You can decompose multi-allelic entries into multiple biallelic entries.

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