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Welcome to the SLRP wiki!

SLRP is a software for long range phasing and IBD detection in inbread and/or isolated populations genotyped on dense SNP arrays. The methodology was described in Palin et.al. 2011. The master branch of this repository contains a further developed version of the software with better user interface (VCF files) and various tricks for phasing thousands of samples (fastPreProc, slice_length, procs, float, IBDcoverLimit options)

• Software requirements
• Command line options
• Examples

If you need help running or installing the software, don't hesitate contact me, Kimmo Palin, at firstname.lastname at sanger.ac.uk

If you use the software in scientific publications, please cite:

Palin, K., Campbell, H., Wright, A. F., Wilson, J. F. and Durbin, R. (2011), Identity-by-descent-based phasing and imputation in founder populations using graphical models. Genetic Epidemiology. doi: 10.1002/gepi.20635

To Do

Here are few things of how to improve SLRP:

• Calculate marginals (forward backward, sum-product), instead of max-marginals (viterbi, max-product) It might even be faster. Scale the values on each node to sum to one and avoid branching like plaque.