66
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Download reference files
To build GREGOR, copy the GREGOR package to the directory you want, and then run the following command:
To build GREGOR, copy the GREGOR package to the directory you want, and then run the following command:
tar xzvf GREGOR.tar.gz
tar xzvf GREGOR.v1.4.0.tar.gz
After you unzip, you can find 3 directories in "GREGOR" (./example ./lib ./script).
After you unzip, in the folder "GREGOR" you can find 4 directories (./Copyrights, ./example, ./lib ./script) and 2 files (README, release_version.txt).
== Download reference files ==
== Download reference files ==
ownload the reference files from this link [http://csg.sph.umich.edu/GREGOR/ GREGOR Download].
Reference files are created for the different population groups(AFR, AMR, ASN, EUR, SAN) from 1000G data (Release date : May 21, 2011).
If your LD r2 threshold equals or greater than 0.7, please download reference files from category: LD window size = 1MB; LD r2 ≥ 0.7.
If your LD r2 threshold equals or greater than 0.2, please download reference files from category: LD window size = 1MB; LD r2 ≥ 0.2.
After unzip, you will get 47 reference files in the directory "~/ref"
After download reference files, you need merge the part files to one gz file. Use the command line likes:
cat \
GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.00 \
GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.01 \
GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.02 \
GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.03 \
GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.04 \
> GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz
Then extract this file:
tar zxvf GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz
You will get one directory which has the name "AFR".
== Basic Usage Example ==
== Basic Usage Example ==
## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
###############################################################################
###############################################################################
INDEX_SNP_FILE = /workingdirectory/example/example.index.snps.rsid.list.txt ## e.g. /workingdirectory/example/example.index.snps.rsid.list.txt
INDEX_SNP_FILE = /workingdirectory/example/example.index.snps.rsid.list.txt
BED_FILE_INDEX = /workingdirectory/example/example.bed.file.index ## e.g. /workingdirectory/example/example.bed.file.index
BED_FILE_INDEX = /workingdirectory/example/example.bed.file.index
REF_DIR = /workingdirectory/ref/ ## reference directory
REF_DIR = /workingdirectory/ref/
R2THRESHOLD = 0.7
R2THRESHOLD = 0.7
LDWINDOWSIZE = 1000000
LDWINDOWSIZE = 1000000
OUT_DIR = /workingdirectory/example/example.rsid.20130808/ ## e.g. /workingdirectory/example/example.rsid.20130808/
OUT_DIR = /workingdirectory/example/example.rsid.20130808/
MIN_NEIGHBOR_NUM = 500
MIN_NEIGHBOR_NUM = 500
BEDFILE_IS_SORTED = True
BEDFILE_IS_SORTED = True
BATCHTYPE = slurm
POPULATION = AFR ## define the population, you can specify EUR, AFR, AMR or ASN
BATCHOPTS = --partition=main --time=0:30:0
TOPNBEDFILES = 2
JOBNUMBER = 10
###############################################################################
#BATCHTYPE = mosix ## submit jobs on MOSIX
#BATCHOPTS = -E/tmp -i -m2000 -j10,11,12,13,14,15,16,17,18,19,120,122,123,124,125 sh -c
###############################################################################
#BATCHTYPE = slurm ## submit jobs on SLURM
#BATCHOPTS = --partition=main --time=0:30:0
###############################################################################
BATCHTYPE = local ## run jobs on local machine
In the config file, there are several parameters to adjust:
In the config file, there are several parameters to adjust:
BED_FILE_INDEX: This file lists the datasets (e.g. BED files) to be used for enrichment analysis. Use complete paths to file locations and make sure positions are in hg19 format.
BED_FILE_INDEX: This file lists the datasets (e.g. BED files) to be used for enrichment analysis. Use complete paths to file locations and make sure positions are in hg19 format.
REF_DIR: Define reference file directory which you download at here.
REF_DIR: Define reference file directory which you download at here. If your "AFR" folder is at "/home/myid/GRGORE/ref/AFR/", then define this parameter to "/home/myid/GRGORE/ref/".
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size.
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size. If you download r2 ≥ 0.7， you can define this number between 1 and 0.7.
OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".
OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".
BEDFILE_IS_SORTED: True or false, depending on whether the BED files listed in the index file are sorted.
BEDFILE_IS_SORTED: True or false, depending on whether the BED files listed in the index file are sorted.
POPULATION: If you use reference file "AFR", define this to AFR. You have 5 optiones: AFR, AMR, ASN, EUR and SAN.
GREGOR can run on local machine or on the cluster with MOSIX or SLURM.
BATCHTYPE: When you run GREGOR on local machine, specify "local"; when run on MOSIX system, specify "mosix"; when run on SLURM system, specify "slurm".
BATCHOPTS: This parameter works with BATCHTYPE when you specify "mosix" or "slurm". For example, when you define mosix, this parameter can be "-E/tmp -i -m2000 -j10,11,12,13,14,15,16 sh -c"; when you define "slurm", it can be "--partition=1000g --time=0:30:0"
BATCHOPTS: This parameter works with BATCHTYPE when you specify "mosix" or "slurm". For example, when you define mosix, this parameter can be "-E/tmp -i -m2000 -j10,11,12,13,14,15,16 sh -c"; when you define "slurm", it can be "--partition=1000g --time=0:30:0"
== Reference Files ==
We provide two kinds of reference files. The difference between these reference data are LD buddy definitions.
*LD window size = 1MB; LD r2 ≥ 0.7：
**All LD buddies are in window size 1MB and r2 is greater than and equals to 0.7. If you want to calculate LD buddies in 1MB and r2 ≥ 0.7 (such as 0.9,0.8,0.7), please use these reference data.
*LD window size = 1MB; LD r2 ≥ 0.2：
**All LD buddies are in window size 1MB and r2 is greater than and equals to 0.2. If you want to calculate LD buddies in 1MB and r2 ≥ 0.2 (such as 0.6,0.5,0.4,0.3,0.2), please use these reference data.
== Results Output ==
== Results Output ==
*Note:
*Note:
**SNPs that cannot be converted from rsID to chr:pos format are listed in the output file rsid.index.snp.txt. SNPs for which there are no LD proxies or no MAF data available are listed in the output file nonannoted.index.snp.txt.
**SNPs that cannot be converted from rsID to chr:pos format are listed in the output file rsid.index.snp.txt. SNPs for which there are no LD proxies or no MAF data available are listed in the output file nonannoted.index.snp.txt.
** If one index SNP and its LD-buddies are not in any bed region, the Pvalue could be defined to "NA"
== Testing GREGOR ==
== Testing GREGOR ==
