SNV impact predictor
Simpred takes a snpEff-generated annotation file and for every SNV except the ones annotated as "modifier" it computes the potential substitution effect (relative to the max possible substitution effect) based on the following sets of descriptors:
- The aaI7 set of descriptors-based effect. [1]
- The Exchangeability of Amino Acids in Proteins. [2]
- The Sneath dissimilarity index. [3]
A gzipped vcf file from the snpEff software.
python3 simpred.py examples/Borneo_sumatra_malaysia_modern_SNPeff_moderate.vcf.gz > output.csv
A csv file containing the result:
| Scaffold | Coord | Ref | Var | Type | Effect | Transcript | Ref_aa | Coord_aa | Var_aa | Ref_aa_abbrev | Var_aa_abbrev | aaI7 | exchgb_ref_var | exchgb_var_ref | sneath_dissim |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sc9M7eS_1_HRSCAF_2 | 362173 | A | C | missense_variant | MODERATE | mRNA20769 | Ile | 46 | Leu | I | L | 0.05 | 0.52 | 0.34 | 0.11 |
| Sc9M7eS_1_HRSCAF_2 | 412292 | T | A | missense_variant | MODERATE | mRNA20769 | Asp | 163 | Glu | D | E | 0.16 | 0.16 | 0.46 | 0.16 |
Note: The exchaneability relation is non-symmetrical and, thus, we provide the value for both reference -> variant (exchgb_ref_var) and the variant -> reference (exchgb_var_ref) substitution.
[1] Rudnicki WR, Komorowski J (2010). Feature Synthesis and Extraction for the Construction of Generalized Properties of Amino Acids. Rough Sets and Current Trends in Computing Vol.3066, ed Tsumoto S., Słowiński R., Komorowski J. G-BJ. (Springer, Berlin, Heidelberg), pp 786-791.
[2] Lev Y. Yampolsky and Arlin Stoltzfus. GENETICS August 1, 2005 vol. 170 no. 4 1459-1472;
[3] Sneath, P. H. (1966-11-01). Relations between chemical structure and biological activity in peptides. Journal of Theoretical Biology. 12 (2): 157-195.