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Question: How does SnpEff calculate effects?
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gravatar for suomenruotsalaiseen
5.0 years ago by
suomenruotsalaiseen • 0
suomenruotsalaiseen • 0 wrote:

In the SnpEff output file you can find possible effects of the variants (frame shift, stop codon gained, splice site etc). I understand, that SnpEff is based on interval forest algorithm, but what is the calculation behind this? Is there a score with minimum and maximum values? I am confused about how SnpEff desides, what effect a SNP has.
snp snpeff variant effect prediction • 2.0k views
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modified 5.0 years ago by Istvan Albert ♦♦ 84k • written 5.0 years ago by suomenruotsalaiseen • 0
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gravatar for Istvan Albert
5.0 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

The interval forest algorithm refers to the efficient representation of the data - it is relevant to the query speed of SnpEff but not to what it does. The effects of the SNPs that can be recognized are tabulated in the SnpEff paper http://snpeff.sourceforge.net/SnpEff_paper.pdf Note how these effects are directly observable attributes that can be obtained by translating the annotated sequence. For example a mutation creates a stop codon in the original reading frame that was not there before. Importantly these are not all the effects that a SNP can have. This tool will report only those effects that are directly reflected in the sequence.
ADD COMMENT • link modified 5.0 years ago • written 5.0 years ago by Istvan Albert ♦♦ 84k
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