https://github.com/jfjlaros/snp

Non-biallelic SNPs for population genetics and forensics.
https://github.com/jfjlaros/snp

dbsnp forensics snp-candidates tri-allelic

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Non-biallelic SNPs for population genetics and forensics.

• Host: GitHub
• URL: https://github.com/jfjlaros/snp
• Owner: jfjlaros
• License: mit
• Created: 2015-06-10T11:53:40.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2018-03-18T19:59:13.000Z (almost 7 years ago)
• Last Synced: 2024-11-13T03:20:54.490Z (2 months ago)
• Topics: dbsnp, forensics, snp-candidates, tri-allelic
• Language: C
• Homepage:
• Size: 7.81 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Finding non-biallelic SNPs

SNPs are used as markers for various population genetic purposes. In particular

non-biallelic SNPs are of interest for identification purposes; to have the

same discriminative power, more biallelic than non-biallelic SNPs are required.

In this project, we present a tool that uses the

[NCBI](http://www.ncbi.nlm.nih.gov/) public database

[dbSNP](https://www.ncbi.nlm.nih.gov/projects/SNP/) to identify non-biallelic

SNPs.

This work was [published](https://www.ncbi.nlm.nih.gov/pubmed/19647708) in

[FSI Genetics](http://www.fsigenetics.com/) in 2009.

## Installation

Install the [expat](http://expat.sourceforge.net/) development files:

    apt-get install libexpat1-dev

Retrieve the source code and compile the program:

    git clone https://github.com/jfjlaros/snp.git

    cd snp/src

    make

## Usage

The program requires a dump of the database in XML format. These files are

typically found in the subfolder named `genotype` of any of the builds hosted

on the [download site](https://ftp.ncbi.nih.gov/snp/organisms/) of the NCBI.

For a file named `gt_chrXX.xml.gz`, use the following command to find the SNP

candidates:

      zcat gt_chrXX.xml.gz | ./snp  > output.txt

The `treshold` parameter is used to specify the minimum allele frequency (in

percentages). If this option is omitted, the threshold defaults to 0. By

increasing this variable the amount of output can be greatly reduced, setting

it to 1 or higher is recommended.

## Related work

Some [notes](dbsnp_allele_frequency.md) on allele frequencies on the X- and

Y chromosomes.

Inspired by this research, we looked into the degradation of

[methylated nucleotides](https://github.com/jfjlaros/cpg) for similar purposes.