Code for the chromatin variation project (Kasowski et al. 2013). 

bin: Mostly preprocessing stuff (alignment/cleaning up of reads, peak calling, signal track
generation, QC etc). In many cases there's two scripts with similar names (eg. alignSample.sh and
alignBatch.sh). In these cases, the "Sample" script does the actual work. The "Batch" script reads
metadata (such as cell line name, factor name etc) and submits jobs that call the "Sample" script.

matlab: Mostly code for computing average signal (calling extractsignal), finding dips (not used in
the paper), and scanning motifs on the personal genomes.

python: Code for creating personal genomes (the add*Snps* files). Various other utilities.

rscripts: Post-processing (plots, statistics etc).

variants: Code for cleaning up the 1000GP genotypes and generating lists of SNPs and indels for each
individual.