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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
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
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.