Sunday, November 30, 2014

Sub Project: Autosomal Pedigree Customization

This is a sub-project for Autosomal Pedigree Creator.

This tool allows to create customized pedigree trees based on different thresholds.

Prerequisites:
Usage:

Copy atree.txt (found in tmp folder after the execution of Autosomal Pedigree Creator) into the root folder of atree2gv and execute the below command from console / command prompt.

atree2gv [-d=<distant-bp-threshold>] [-c=<close-bp-threshold>] [-s=<individual-segment-bp-threshold>] [-g=<large|small>]

E.g.,
atree2gv -d=1000000 -c=1500000000 -s=5000000 -g=large

  • -d=<value>, where value is the threshold in base-pairs for defining distant cousins.
  • -c=<value>, where value is the threshold in base-pairs for defining close relations, usually parent/child. If there are no parent child but only 2nd or third cousins, then you need to enter the value in base-pairs that could be shared by those relations. Parent/child shares 50% of 3.2 billion base pairs. So, the default value is 1500000000.
  • -s=<value>, where value is the threshold in base-pairs for defining individual segments.

Download atree2gv.zip (11.9 MB)

Source Code at GitHub.

License: MIT License.