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After unzip, copy all reference files to directory "./ref"
After unzip, copy all reference files to directory "./ref"
== Basic Usage Example ==
When you run
perl FallInBed.pl
you will get some information about FallInBed
----------------------------------------------------------------------------------
FallInBeds.pl : Functional annotation of trait-associated variants
----------------------------------------------------------------------------------
This program tests for enrichment of an input list of trait-associated index
SNPs ([chr:pos] format or rsID, hg19) in experimentally annotated regulatory
domains (BED files).
Note: the index SNPs should be hg19 version. All maf and LD data are from 1000G
EUR samples! (Release date : May 21, 2011)
Version : 1.1.0
Report Bug(s) : jich[at]umich[dot]edu
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Usage : perl FallInBeds.pl --conf [conf.file]
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The following command is a typical command line:
perl FallInBed.pl --conf [conf.file]
Example configuration file can be found in example directory. Users have to modify the configurations before running.
== Configuration File ==
The example configuration file below illustrate how to configure the FallInBed configuration file.
##############################################################################
# CHIPSEQ ENRICHMENT CONFIGURATION FILE
# This configuration file contains run-time configuration of
# CHIP_SEQ ENRICHMENT
###############################################################################
## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
###############################################################################
INDEX_SNP_FILE = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.index.snps.rsid.list.txt ## e.g. /home/myid/data/FallInBed/example.snp.txt
BED_FILE_INDEX = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.bed.file.index ## e.g. /home/myid/data/FallInBed/bedfiles.index
R2THRESHOLD = 0.7
LDWINDOWSIZE = 1000000
OUT_DIR = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.rsid.20130808/ ## e.g. /home/myid/data/FallInBed/result/
MIN_NEIGHBOR_NUM = 500
BEDFILE_IS_SORTED = true
MOSRUN = mosbatch -E/tmp -i -m2000 -j20,43,122,135,137,138,149,151,153,154,155,156,162,163 sh -c
In configure file, there are 10 parameters.
INDEX_SNP_FILE: define the index SNP file. In this file, there is only one column without header. Index SNP can be rsid or chr/pos format.
BED_FILE_INDEX: define the bed files.
R2THRESHOLD and LDWINDOWSIZE: these two parameters are defined the LD buddy.
RANDOM_LIST_NUM: define how many random lists, e.g. 100 or 1000
OUT_DIR: All result files are saved to this folder. In this folder, script will create multi-subdirectories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".
MIN_NEIGHBOR_NUM: define neighbor number around index SNP. Script will find no less than this number around every index SNP.
== Acknowledgements ==
FallInBed is a result from collaborative effort by Cristen Willer, Jin Chen, Ellen Marie Schmidt
, He Zhang, and Goncalo Abecasis. Please email to Cristen Willer [cristen@umich.edu ] for any questions.
