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.
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.