nbisweden/simpred

SNV impact predictor

simpred

SNV impact predictor

Synopsis

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:

1. The aaI7 set of descriptors-based effect. [1]
2. The Exchangeability of Amino Acids in Proteins. [2]
3. The Sneath dissimilarity index. [3]

Input

A gzipped vcf file from the snpEff software.

Usage

python3 simpred.py examples/Borneo_sumatra_malaysia_modern_SNPeff_moderate.vcf.gz > output.csv

Output

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.

References

[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.

simpred's Issues

No example data for simpred in repository - no citation

Dear simpred developers,

I am interested in working with simpred on my data. The README document says we can use the output of SnpEff and example command for usage is python3 simpred.py examples/Borneo_sumatra_malaysia_modern_SNPeff_moderate.vcf.gz > output.csv . However there is no "example" folder in the git repository and no data to work with. I tested simpred in one of my gzipped annotated files output from SnpEff and it did not work. Would you please provide some example data to see how to modify my archive and how simpred works?

Also, I have seen that there is no citation associated to this software and it was hard to find papers where they worked with it. Has it been tested in other data?

Best regards and thanks,
Carlos Sarabia