ChromoPainter is a tool for finding haplotypes in sequence data. Each individual is "painted" as a combination of all other sequences. It can output a range of features, including:
- Sample haplotypes
- Expectations of the number of recombination events at all sites
- A wide range of related features
ChromoCombine is a tool to help manage the large number of files generated when running ChromoPainter in parallel on a large number of separate compute nodes. You can place all these files into a single directory and ChromoCombine will calculate the correct way to combine them. It also calculates the effective number of chunks (i.e. the c value).
fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data. By using the output of ChromoPainter as a (nearly) sufficient summary statistic, it is able to perform model-based Bayesian clustering on large datasets, including full resequencing data, and can handle up to 1000s of individuals. Full assignment uncertainty is given.
The pipeline for every analysis is:
ChromoPainter-> ChromoCombine->fineSTRUCTURE MCMC->fineSTRUCTURE tree creation.
They are installed in /usr/local/chromopainter. The executables are in /usr/local/chromopainter/bin. Users should add the following to their .bashrc or .cshrc files:
export PATH=/usr/local/chromopainter/bin:$PATH (bash users) export LD_LIBRARY_PATH=/usr/local/gsl/64/lib:$LD_LIBRARY_PATH setenv PATH /usr/local/chromopainter/bin:$PATH (csh or tcsh users) setenv LD_LIBRARY_PATH /usr/local/gsl/64/lib:$LD_LIBRARY_PATH
Set up a batch script along the following lines:
#!/bin/bash #PBS -m be cd /data/username/chromodata chromopainter -g geno.filein -r reconmap.filein - f donorlist.filein [options] chromocombine [options] -o output file1 file2 file3.... finestructure [options] datafile initialpopfile > outputfile
Typing 'chromopainter -h', 'chromocombine', or 'finestructure' on the command line will print usage info, including options and required inputs, to the screen.
Set up a swarm command file along the following lines:
# --- this file is called chromo.swarm -------------------------- chromopainter -g geno1.filein -r reconmap1.filein - f donorlist1.filein [options] chromopainter -g geno2.filein -r reconmap2.filein - f donorlist2.filein [options] chromopainter -g geno3.filein -r reconmap3.filein - f donorlist3.filein [options] [...]
swarm -f chromo.swarm