biofold/fido-snp repository overview

INTRODUCTION

Emidio Capriotti, 2018. University of Bologna Scripts are licensed under the Creative Commons by NC-SA license.

Fido-SNP is a program for the annotation of single nucleotide variants in the dog genome.

Please cite: Capriotti E, Montanucci L, Profiti G, Rossi I, Giannuzzi D, Aresu L, Fariselli P. (2019). Fido-SNP: The first webserver for scoring the impact of single nucleotide variants in the dog genome. Nucleic Acids Research. DOI:10.1093/nar/gkz420.

HOW TO RUN

Fido-SNP can take in input a single variation or a file containing multiple single nucleotide variants.

• For single variants use the option -c: python fido_variants.py chr1,15189413,C,G -g canfam3 -c

• For input file the input can be either:

  plain tab separated file with 4 columns: chr, position, ref, alt python fido_variants.py test/test_canfam3.tsv -g canfam3

  vcf file with in the first 5 columns: chr, position, rsid, ref, alt
  python fido_variants.py test/test_canfam3.tsv.gz --vcf -g canfam3

OUTPUT

Fido-SNP returns in output a probabilistic score between 0 and 1. If the score is >0.5 the variants is predicted as disease related. The probability is added as an extra column to the input file. An example of output is reported below.

1       15189413        C       G       Yes     Pathogenic    0.515   0.075  -0.027   0.317
5       34700967        T       A       Yes     Benign        0.145   0.242   0.766   0.678
9       54071528        T       C       Yes     Benign        0.327   0.246  -0.402   0.260