Software

vcf2fc.py is a python script to calculate Fc described in Fujito et al.(2018) for detecting positive selection on a SNP site of interest.

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README

We appreciate Dr. Kosuke Teshima from Kyushu University for modification of this script

Requirements:

・Python 3

Inputs:

・ID of the SNP of interest (“core SNP”).

・A VCF file of the genomic region surrounding the core SNP.

* Phased genotypes are required.

* Note that the input VCF file should contain only individuals belonging to the population in which you are trying to detect positive selection.

* The VCF file should contain a sufficiently large genomic region which covers the entire high LD region around the core SNP. We recommend starting from 500kb or 1Mb, and if you get an error message, then use a larger region.

Usage:

$python vcf2fc.py input.vcf rsXXX

The first argument after “vcf2fc.py” is the VCF file (e.g. input.vcf) and the second argument is the ID of the core SNP (e.g. rsXXX).

Output:

An example output is shown below.

Fc value and location of the central region are at the bottom of the output.

Example output:

Reading the vcf file...

  target SNP   rs4988235

  target position   136608646

calculating LD...

max(r^2) is  0.9191

Threshold is  0.0919

Candidate core region should be between  136474541 136827600

Calculating Fc...

Done.

10 Fc values from the smallest

[start pos, end pos] Fc

[136602491, 136652045] 0.0059

[136552188, 136652045] 0.0061

[136552517, 136652045] 0.0062

[136552526, 136652045] 0.0062

[136554797, 136652045] 0.0062

[136555484, 136652045] 0.0062

[136555525, 136652045] 0.0062

[136545844, 136652045] 0.0062

[136546927, 136652045] 0.0062

[136552188, 136640787] 0.0063

Fc = 0.0059

core region = [136602491, 136652045]

Please contact satta@soken.ac.jp for any questions.

(June 12 2019)