Friday, June 28, 2013

OpenSNP Analyzer


This tool is now obsolete as there is no potential use for it. 
It is one of the very first tools developed.


OpenSNP analyzer helps to extract the genes/mutations on genes responsible for a particular phenotype using the downloads provided by OpenSNP which includes genotypes of several volunteers. The software supports both FTDNA and 23andme data files. One special requirement is that, all files must be of same build level. Please use Build 36 to 37 Converter if you wish to convert your build 36 raw data files before using this tool.

How does OpenSNP analyzer works? It takes the common genes of a folder containing samples of the same phenotype, then it takes the common genes of a folder containing samples of not having the phenotype of the first folder, then subtracting the second folder which do no have a phenotype from the first folder with phenotype could extract genes that may be responsible for that particular phenotype.

Prerequisites: Microsoft .Net Framework 4.0

Usage:
Syntax:
        osnp <folder1-genotypes> <folder2-genotypes>

E.g,
        osnp C:\P_Reaction\ C:\P_NoReaction\

Output:
The program will generate 4 files:
  • <folder1-genotypes>.same - contains all matching genes within <folder1-genotypes> directory
  • <folder2-genotypes>.same - contains all matching genes within <folder2-genotypes> directory
  • <folder1-genotypes>_minus_<folder2-genotypes>.extract - contains all matching genes when <folder2-genotypes>.same is subtracted from <folder1-genotypes>.same
  • <folder2-genotypes>_minus_<folder1-genotypes>.extract - contains all matching genes when <folder1-genotypes> is subtracted from <folder2-genotypes>.same
Download : osnp.exe (14 Kb)

Source Code at GitHub.

Change Log
Version 1.3
  • Minor Bug fix.
Version 1.2
  • Allows comparison when chromosome data is missing.
Version 1.1
  • Bug fix.
Version 1.0
  • Initial release.

Tuesday, June 25, 2013

Y-Haplogroup Predictor

There are many haplogroup predictors but why this one? This Y-Haplogroup Predictor is unique in the sense it uses artificial intelligence for prediction. The neural network it uses is based on Back Propagation Network with Momentum having a normalized input of 48 bits, a hidden layer of 72 neurons and a normalized output of 5 bits. It had been trained to a level of net error 0.01203 using Neuroph.

Prerequisites: Java 7

Usage:
If you have JRE 7.0 installed and available on path, you can just double click on it. Then, just enter the 12 Marker STR values and click Predict Haplogroup.
You can also run the Jar file as follows:
C:\Downloads> java -jar yhaplo.jar


Download : yhaplo-predictor.jar (240 Kb)

Source Code at GitHub.

Change Log for ver 1.0:
  • Supports all major haplogroups. Subclades not yet supported.

Monday, June 24, 2013

Y-HaploGroup Population Browser

In human genetics, the haplogroups most commonly studied are Y-chromosome (Y-DNA) haplogroups and mitochondrial DNA (mtDNA) haplogroups, both of which can be used to define genetic populations. Y-DNA is passed solely along the patrilineal line, from father to son, while mtDNA is passed down the matrilineal line, from mother to offspring of both sexes.

This software allows browsing and reporting of different population and their Y-chromosome (Y-DNA) haplogroups similarities and comparisons. All details are collected from Wikipedia and the reference for it will be available on the Wikipedia page.

Prerequisites: Java 5.0+

Usage: If you have installed JRE 5.0 or above and available on path, you can just double click on it.
C:\Downloads> java -jar haplogroup-browser.jar

Screenshot:

Download : haplogroup-browser.jar (5 Mb)

Source Code at GitHub.

Change Log for ver 1.0:
  • A Simple Y DNA Haplogroup Browser.

SNPs Extractor


This tool is now obsolete as there is no potential use for it. 
It is one of the very first tools developed.


This project is to find genes that are responsible for a particular phenotype which must be used with OpenSNP. It supports both FTDNA and 23andMe raw data files.

Prerequisites: Microsoft .Net Framework 4.0

Usage:
Syntax:
snpsextract <file1> <file2> <out_file> [DIFF]

E.g,
snpsextract user_000.txt user_001.txt common_snps.txt
snpsextract user_000.txt user_001.txt diff_snps.txt DIFF

Download : snpsextract.exe (12 Kb)

Source Code at GitHub.

Change Log
Version 1.2
  • Bug fixes, changed name as it supports FTDNA raw data as well.
Version 1.1
  • Much faster comparison.
Version 1.0
  • Finds similar or different genes in 23andMe format.

Saturday, June 22, 2013

X-DNA Relationship Path Finder


The estimate by this tool is not very accurate, as accurate estimates are not possible in X-DNA.


The aim of this project is to find the relationship path of a common ancestor with someone who you share X-DNA. When you share autosomal DNA and X-DNA with a match, based on the how much you share an autosomal DNA and using the unique inheritance pattern of X-DNA, the possible inheritance path can be arrived. It also has a debugging mode to explain how much DNA is passed on. The value in curly brackets is the shared cM passed on. A PDF document is attached explaining shared autosomal DNA vs X DNA inheritance from common ancestor.

Prerequisites: Microsoft .Net Framework 2.0

Usage:  There are two ways to use it. The easiest and simplest is to just execute the program which opens the interactive options allowing you to enter values one by one. You can also give the options as arguments.
Syntax:
xpathfinder <Autosomal Total cM> 
            <X Total cM> 
            <YourGender> 
            <MatchGender> 
            [DEBUG]

E.g,
xpathfinder 34.6 10 M F

If you wish to enable debugging (to understand how the relationship path is arrived), you can add an additional argument called DEBUG)
E.g,
xpathfinder 34.6 10 M F DEBUG

If you would like to send the output to a file and use the redirection
E.g,
xpathfinder 34.6 10 M F DEBUG > output.txt

Download : xpathfinder.exe (17 Kb), based on X-Inheritance cM Chart.pdf

Source Code at GitHub.

Change Log for ver 1.0:
  • Console based, accepts arguments as well as interactive.

Autosomal DNA Converter (Windows)

The aim of this project is to enable the conversion of different data formats for autosomal DNA file. Supports the conversion of raw autosomal dna data from ftdna, 23andme, ancestry and decodeme to ftdna, 23andme and ancestry.

Prerequisites: Microsoft .Net Framework 4.0

Usage:
Syntax:

        aconv <in-file> <out-file> [options]

Optional Parameters:
 -i  [Input Type]  - Value can be detect,ftdna,23andme,decodeme,
                     geno2 or ancestry. This values is optional and 
                     not required. Use only if autodetect fails.
                     Default is detect
 -o  [Output Type] - Value can be ftdna,23andme,geno2,ancestry, 
                     plink or eigenstrat. Default is ftdna

Example:
    aconv 264652-o36-results.csv.gz 23andme.txt -o 23andme

Note: Converting to FTDNA from 23andme or ancestry will lose Y and mtDNA data as they are not part of raw download format. Converting Geno 2.0 to anything will not have build positions, but just a format change.

Download : aconv.exe (19 Kb)

Microsoft .Net 4.0 is installed by default on most of the windows operating system. If you don't have .Net version 4.0 you can use aconv.exe (20 Kb) version 1.3 compiled with Microsoft .Net 2.0.

Source Code at GitHub.

Change Log
Version 1.4:
  • Support for plink and eigenstrat.
Version 1.3:
  • Support for extremely large files. Fixed Out of memory issue.
Version 1.2:
  • Basic support for Geno 2.0 conversion to another format. Since Geno 2.0 does not have any build positions, the output format will also not have any build positions.
Version 1.1:
  • Auto-detects input file. Supports ftdna, 23andme, ancestry and decodeme. Also supports compressed .gz files.
Version 1.0:
  • Converts FTDNA Autosomal DNA (FamilyFinder) raw download file format to 23andMe format.