Monday, July 22, 2013

Phasing Utility

Phasing is the task or process of determining the parental source of a SNP's alleles. A simpler way to put it, it is the process of trying to determine which DNA came from the mother, and which came from the father. The term is usually applied to types of DNA that recombine, such as autosomal DNA or the X-chromosome. The benefit of phasing is being able to identify which ancestor a segment was inherited from (Ref: isogg.org). This is a simple utility that helps to extract the SNPs of the other parent if one parent and a child is provided.

Prerequisites: Microsoft .Net Framework 4.0

Usage: Select the child's, atleast one parent's autosomal file and click phase. Then click download to get the phased files for parents and child.

Screenshot:


Download : PhasingUtility.exe (49 Kb)

Source Code at GitHub.

Change Log
Version 1.5
  • Bug fix.
Version 1.4
  • Minor bug fix.
Version 1.3
  • Bug fix. 
Version 1.2
  • Phasing output now includes parents. Introduced user friendly interface.
Version 1.1
  • Major Bugfix.
Version 1.0
  • Initial Release.

Sunday, July 14, 2013

Ancestral Cousin Marriages


Cousin marriage between parents can be calculate using Pedigree Collapse Calculator. Hence, this tool is now obsolete.


Ancestral Cousin Marriages is a tool to find if there are any cousin marriages for a particular DNA. It also calculates cousin relationship between each parent. It is based on Runs of Homozygous and the long shared segments in cousins. It supports both build 36 and build 37. FTDNA Family Finder and 23andMe raw data can be used as input.

Prerequisites: Microsoft .Net Framework 4.0

Usage:
Syntax:

        acousm <input-file> [options]

Optional Parameters:
 -c     Cousin Limit. Default is 5, Max value is 16.
 -s     SNP Threshold. Default is 500.
 -g     Gender of input file. Values can be M for
        male, F for female and U for unknown. Default is U.
 -m     Minimum threshold for cM. Default is 1.
 -d     Debugging and/or Additional Information.
        Default is false

E.g,
acousm <12345-results.csv>


Download : acousm.exe 33 MB)

Source Code at GitHub

Change Log
Version 1.1
  • Bug fixes.
Version 1.0
  • Initial release.

Wednesday, July 10, 2013

Build Converter


This tool is replaced by Assembly Converter which can convert from/to all builds, even the unreleased future builds using LiftOver chain files.


Simple program that converts FTDNA family finder and 23andMe Autosomal raw files from build 36 to 37.

Prerequisites: Microsoft .Net Framework 4.0

Usage:
Syntax:
        b36to37 <input-file> <output-file> [-r]

-r = Reverse transformation. i.e., convert build 37 back to build 36.

E.g,
b36to37 12345-autosomal-o36-results.csv 12345-autosomal-o37-results.csv
b36to37 12345-autosomal-o37-results.csv 12345-autosomal-o36-results.csv -r

Download : b36to37.exe (58 MB)

Source Code at GitHub.

Change Log
Version 1.2
  • Reverse functionality added. i.e., Build 37 back to build 36.
Version 1.1
  • Added Friendly messages.
Version 1.0
  • Autodetects and converts build 36 to 37.

My Health


Note: This application does not provide you any medical advise. It is purely developed and provided free from a hobbyist perspective. Please visit a physician if you require any medical advice.

My own suggestion/opinion: Genetics will never reveal 100% of your health. Even if you have a gene for a particular disease, you can completely avoid it by following good and healthy life-style and can pass on to offspring. This new field is called Epigenetics.


My-Health allows you to quickly check your health details available in your DNA. All health related SNP details are fetched from SNPedia. This is not a comprehensive report but does include the important and interesting genotypes. For a comprehensive report, please use Promethease from SNPedia. This application does not provide you any medical advise - developed and provided free from a hobbyist perspective. Please visit a physician if you require any medical advice.

Prerequisites: Microsoft .Net Framework 4.0

Usage: Just double click on it, open a FTDNA Family Finder or 23andMe autosomal raw data.

Screenshot:

Download : MyHealth.exe (408 Kb)

Source Code at GitHub.

License: According to SNPedia, Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License, I attribute that the data used is from SNPedia. This product is not for any commercial or financial benefit and according to share-alike terms, it is licensed on the same terms of CC BY-NC-SA 3.0 US.

Change Log for ver 1.0:
  • SNPedia data as on 9th July 2013

Tuesday, July 9, 2013

X Compare

This tool compares two Family Finder FTDNA X chromosome raw data or X chromosome of autosomal 23andMe raw data files and provides the shared segments. It also provides an estimated common ancestor. It supports only build 37. Please use Build-36-to-37 tool to convert to 37 if you have build 36.

Prerequisites: Microsoft .Net Framework 4.0

Usage:
Syntax:

        xcmp -i <input-file> -m <match-file> [options]

Optional Parameters:
 -g  [Gender]           - Value can be M for male, F for female
                          Default is M.
 -nc [Match NoCall]     - Value can be true or false. Default is true
 -t  [Unit Type]        - Value can be cM for centimorgans or Mb for megabase,
                          Default is cM
 -er [Error Radius]     - Default is -1 (Disabled).
 -s  [SNP Threshold]    - Default is 150
 -cm [cM Threshold]     - Used when type is cM, Default is 1
 -mb [Mb Threshold]     - Used when type is Mb, Default is 1
 -o  [Output File]      - Send output to file. Default is console.
 -nt [Not Tested]       - Consider missing SNPs in input that exist in match
                          file as, 0 = Doesn't exist in match, 1 = Existing in
                          input, 2 = No-match. Default is 0

E.g,
xcmp -i <12345-x-results.csv> -m <98765-x-results.csv>

Download : xcmp.exe (261 Kb)

Source Code at GitHub.

Change Log
Version 1.1
  • Bug Fixes.
Version 1.0
  • Compares in both Mb and cM.
Acknowledgements and References

Autosomal Compare


This tool is replaced by Autosomal Segment Analyzer.


This tool compares two Family Finder FTDNA or Autosomal 23andMe raw data files and provides the shared segments. The comparison logic is based on David Pike's tool. It supports both build 36 and build 37. FTDNA Family Finder and 23andMe raw data can be used as input.

Prerequisites: Microsoft .Net Framework 4.0

Usage:
Syntax:

atcmp <input-file> <match-file> [options]

Optional Parameters:
-g  [Gender]           - Value can be M for male, F for female
and U for unknown. Valid only if unit
type is cM. Default is U.
-nc [Match NoCall]     - Value can be true or false. Default 
is false
-t  [Unit Type]        - Value can be cM for centimorgans or Mb
for megabase, Default is cM
-er [Error Radius]     - Default is -1 (Disabled).
-s  [SNP Threshold]    - Default is 500
-p  [Cousin Marriages] - Probe for cousin relationship. Value
can be 1 for 1st cousin marriages and
up to 16 for 16th cousin marriages. 
Default is disabled.
-cm [cM Threshold]     - Used when type is cM, Default is 1
-mb [Mb Threshold]     - Used when type is Mb, Default is 1
-o  [Output File]      - Send output to file. Default is
console.
-ca [Out Ancestor File]- Construct the DNA of common ancestor
for input and the provided match.
-nt [Not Tested]       - Consider missing SNPs in input that
exist in match file as, 0 = Doesn't
exist in match, 1 = Existing in input,
Default is 0

E.g,
atcmp <12345-results.csv> <98765-results.csv>

Download : atcmp.exe (33 MB)

Source Code at GitHub

Change Log
Version 1.5
  • Minor bug fix.
Version 1.4
  • Identify Build error when Mb is used - fixed.
Version 1.3
  • Probe for cousin relationship between parents of input and matches using RoH.
Version 1.2
  • Bug fixes. Build auto-detection. Built-in build 36 and 37 support for cM calculation.
Version 1.1
  • Bug fixes.
Version 1.0
  • Compares in both Mb and cM.

Known Issues and workaround:
Unhandled Exception: System.IndexOutOfRangeException
There seems to be chromosome "0" in some build 37 files from FTDNA which is causing the problem. Removing those lines fixes the issue. I will prepare a fix, until then, you can simply remove those lines before using the tool.

Acknowledgements and References

Thursday, July 4, 2013

My Y-SNP Tree


This tool is replaced by ISOGG Y-Tree 2014, which is again replaced by ISOGG Y-Tree AddOn for Google Chrome


My Y-SNP Tree allows you to mark the y-SNP on the y-tree. It is helpful to understand how your markers fit on the tree.

Prerequisites: Microsoft .Net Framework 4.0

Usage: Just double click on it, paste your y-SNPs on the textbox provided and click 'Mark on Tree'.

Screenshot:

Download from Google Drive.

License: According to ytree.ftdna.com's Attribution NonCommercial ShareAlike 3.0 license, I attribute the Y-Tree data used is from FamilyTreeDNA. This product is not for any commercial or financial benefit and according to share-alike terms, it is licensed on the same terms of CC BY-NC-SA 3.0 as in ytree.ftdna.com.

Change Log
Version 1.1
  • Duplicate names of haplogroups in the tree removed.
Version 1.0
  • Y-SNP tree based on FTDNA draft tree as on 3rd July 2013

Tuesday, July 2, 2013

DIY Dodecad 2.1 Wrapper

A simple wrapper program for DIY Dodecad 2.1 by Dienekes that wraps the program into a simple, self-contained and portable executable. No additional installation required. Supports FTDNA, 23andMe, Ancestry, deCODE and Geno 2.0.

Prerequisites: Microsoft .Net Framework 4.0

Usage: Just execute it, open the file and click calculate (or) just drag and drop any autosomal file.

Screenshot:


Download : DIYDodecadWrapper_1_3.exe (64 MB)

Source Code at GitHub.

Change Log
Version 1.3
  • Bug fix for Ancestry raw data files.
Version 1.2
  • Supports FTDNA, 23andMe, Ancestry, deCODE and Geno 2.0
Version 1.1
  • Included the following calculators apart from dv3: globe13, africa9, eurasia7, euro7, globe10, globe4, K10a, K12b, K7b, weac, weac2, world9
Version 1.0
  • Initial Build, Pie-chart output. DIY Dodecad 2.1 embedded inside.