IBD_Stitch

IBD_Stitch: Sequential construction of IBD states among multiple individuals

1. Overview

The ibd_stitch program constructs IBD states among multiple individuals using a PAC (product-of-approximate-conditionals) likelihood approach. Chris Glazner's Haskell ibd_stitch code is available from this github site.
Latest release, June 25, 2014.

Other Glazner software relating to IBD inference is also available on this site.

2. Installation

The following installation helpful instructions were provided by Hiep Nguyen, December 2015.
Note that Redhat7 was needed: installation under older Redhat versions was not possible.
Note that ``$'' below is the linux/unix prompt.
1. ibd_stitch.cabal requires GHC compiler and Cabal (a package install and build tool)
I chose to install them with rpm packages and installed them on Redhat 7.2 64bit. The package names are:
  • cabal-dev-0.9.2-1.el7.x86_64.rpm
  • cabal-install-1.16.1.0-1.el7.x86_64.rpm
  • ghc-XXX.rpm (approximately 50 packages)
2. Make sure gsl and gsl-devel are installed
3. Make sure lapack and lapack-devel are installed
4. install cabal-install, cabal-dev and happy program:
  • $ cabal update
  • $ cabal install cabal-install
This will create ~/.cabal/bin/cabal executable file

Then

  • $ ~/.cabal/bin/cabal install cabal-dev
  • $ ~/.cabal/bin/cabal install happy
These will create cabal-dev, happy, lens executable files in~/.cabal/bin/ directory
5. Add ~/.cabal/bin/ to your path.
For example in bash:
  • $ export PATH=$PATH:~/.cabal/bin/
6. Compile ibd_stitch
Get ibd_stitch-master.zip from https://github.com/cglazner/ibd_stitch
  • $ unzip ibd_stitch-master.zip
This will create ibd_stitch-master directory

Then

  • $ cd ibd_stitch-master
  • $ ~/.cabal/bin/cabal-dev install
This will create ibd_stitch executable file for you in ibd_stitch-master/cabal-dev/bin/

3. Tutorial and Examples

ibd_stitch is invoked with a single parameter file, which in turn specifies a required marker data file. For examples of these files, and information on running the program and interpreting the output, please see the tutorial. The tutorial is based on text provided by Fiona Grimson.

The tutorial and decribed example files are also available in a gzipped tar file.

These examples have been tested on several operating systems, but please be aware they are not robust. Whether due to the alternate Haskell installations, or to the program itself, some apparently identical parameter files will not run on some systems. It is possible the code references unitialized space, but the problem appears to be in reading the parameter file and setting up the logfile. In the parameter file, some forms of white space (e.g. tab) and/or use of default file names (you are advised to specify your logfile explicitly) can cause problems on some systems.


UW - Statistics: Thursday, 25-Jul-19 Contact: Elizabeth Thompson <eathomp@u.washington.edu>