Scripts:

* 0.define.proximal.distal.regions.pl
	Generating distal/proximal regions for provided interval annotations (based on GENCODE data). 

* Define conserved annotation categories using polymorphisms data. 

1. Define conserved annotation categories from scratch (hg19). 
	1.1.Randomization.pl
		The program using element-sliding method to generate null distributions for fraction of rare variants for each category.
	1.2.FDR.r 
		FDR calculation for the randomization. This script can also output significant categories based on FDR.

2. Define novel conserved regions upon those defined in Khurana et al., (Science 2013).Only applicable to small number of categories, ~ 5. 
	2.sensitive.regions.delta.increment.pl
		The input polymorphisms used in the paper is ' SNP.lowcov.noncodingGENCODE7.1kgMask.bed'.

* 3.gencode.process.pl
	This script processes GENCDOE gtf file to obtain 'promoter','cds','intron' and 'utr' region files, which are used by variants prioritization part. 

* 4.network.analysis.r
	This script generates network centralities for input network (degree or betweenness).

* 5.PWM.score.cut.pl
	This script generates the 'motif.score.cut' file for the variants prioritization part. TFMpvalue-pv2sc in 'TFM-pvalue' package is used to generate sequence score cut-offs for defined p-value cut-off. The file 'motif.score.cut' is used to speed up the gain-of-motif analysis.