Tuesday, July 9, 2013

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