This directory contains genome-wide ARGweaver results for the analysis on
54 unrelated genomes from Complete Genomics.

The raw output from all non-burnin reps is found in the direcory raw_output. 
Note that it is size 280Gb and contains 275,200 files (one for each MCMC rep
and each of 1376 genome segments). To download the whole set, retrieve the
file raw_output_files.txt. Then use the following command:

wget --quiet -i raw_output_files.txt -r -nH --cut-dirs=1

Alternatively, the file cg_results.bed.gz contains all results condensed into a
sorted and indexed bed file. The format is chrom,chromStart,chromEnd,sampleNumber,
tree (newick format).  The recombination events leading from one tree to the next 
within a sample is encoded as a NHX comment in the tree string of the tree to the left of the 
recombination event.

This file is indexed by tabix. Using tabix, any region of the genome can be queried
without downloading the whole file. For example:

tabix http://compgen.bscb.cornell.edu/ARGweaver/CG_results/download/cg_results.bed.gz chr4:123456-123456

will retrieve the trees for all samples in this region.

The ARGweaver software also comes with a utility, arg-summarize, which uses this file
to compute various statistics of the tree in a region. The argWeaver source code,
including arg-summarize, can be downloaded here:

https://github.com/CshlSiepelLab/argweaver

Arg-summarize also has a web interface, available here:

http://compgen.bscb.cornell.edu/ARGweaver/CG_results/

Please do not use the web interface for genome-wide or large queries. It may time out
after 10 minutes, and jobs may be killed if too many are running simultaneously.

Note that extracting statistics across so many trees is computationally complex, and the
web interface may be too slow for large genetic regions. Therefore, some statistics
are available precomputed genome-wide in bigwig format. They are:

tmrca
total-branchlen
popsize

each is available for all individuals, as well as african, asian, and european subsets.
The subsets consist of populations with little evidence of admixture. Specifically,
african: LWK, MKK, YRI populations (17 individuals total)
asian: CHB and JPT populations (8 individuals total)
european: CEPH, CEU, and TSI populations (13 individuals total)