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GREGOR (view source)

Revision as of 17:39, 15 November 2016

1,638 bytes added ,  17:39, 15 November 2016
→‎Download reference files
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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:
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   tar xzvf GREGOR.tar.gz
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   tar xzvf GREGOR.v1.4.0.tar.gz
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After you unzip, you can find 3 directories in "GREGOR" (./example ./lib  ./script).
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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 ==
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ownload the reference files from this link [http://csg.sph.umich.edu/GREGOR/  GREGOR Download].
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Download the reference files from this link [http://csg.sph.umich.edu/GREGOR/  GREGOR Download], then un-package the file
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Reference files are created for the different population groups(AFR, AMR, ASN, EUR, SAN) from 1000G data (Release date : May 21, 2011).
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  tar xzvf GREGOR.ref.tar.gz
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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.
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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.
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After unzip, you will get 47 reference files in the directory "~/ref"
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After download reference files, you need merge the part files to one gz file. Use the command line likes:
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  cat \
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    GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.00 \
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    GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.01 \
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    GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.02 \
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    GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.03 \
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    GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz.part.04 \
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    > GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz
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Then extract this file:
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  tar zxvf GREGOR.AFR.ref.r2.greater.than.0.2.tar.gz
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You will get one directory which has the name "AFR".
    
== Basic Usage Example ==
 
== Basic Usage Example ==
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   ## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
 
   ## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY
 
   ###############################################################################
 
   ###############################################################################
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   INDEX_SNP_FILE = /workingdirectory/example/example.index.snps.rsid.list.txt    ## e.g. /workingdirectory/example/example.index.snps.rsid.list.txt
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   INDEX_SNP_FILE = /workingdirectory/example/example.index.snps.rsid.list.txt
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   BED_FILE_INDEX = /workingdirectory/example/example.bed.file.index ## e.g. /workingdirectory/example/example.bed.file.index
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   BED_FILE_INDEX = /workingdirectory/example/example.bed.file.index  
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   REF_DIR = /workingdirectory/ref/ ## reference directory
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   REF_DIR = /workingdirectory/ref/
 
   R2THRESHOLD = 0.7
 
   R2THRESHOLD = 0.7
 
   LDWINDOWSIZE = 1000000
 
   LDWINDOWSIZE = 1000000
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   OUT_DIR = /workingdirectory/example/example.rsid.20130808/ ## e.g. /workingdirectory/example/example.rsid.20130808/
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   OUT_DIR = /workingdirectory/example/example.rsid.20130808/
 
   MIN_NEIGHBOR_NUM = 500
 
   MIN_NEIGHBOR_NUM = 500
 
   BEDFILE_IS_SORTED = True
 
   BEDFILE_IS_SORTED = True
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   BATCHTYPE = slurm
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   POPULATION = AFR  ## define the population, you can specify EUR, AFR, AMR or ASN
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   BATCHOPTS = --partition=main --time=0:30:0
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  TOPNBEDFILES = 2
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  JOBNUMBER = 10
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  ###############################################################################
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  #BATCHTYPE = mosix ##  submit jobs on MOSIX
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  #BATCHOPTS = -E/tmp -i -m2000 -j10,11,12,13,14,15,16,17,18,19,120,122,123,124,125 sh -c
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  ###############################################################################
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  #BATCHTYPE = slurm   ##  submit jobs on SLURM
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   #BATCHOPTS = --partition=main --time=0:30:0
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  ###############################################################################
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  BATCHTYPE = local ##  run jobs on local machine
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In the config file, there are several parameters to adjust:
 
In the config file, there are several parameters to adjust:
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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.
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REF_DIR: Define reference file directory which you download at here.
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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/".
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R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size.
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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".  
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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.
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BATCHTYPE: We have three options for this parameter. When you run GREGOR on local machine, specify "local"; when run on MOSIX system, specify "mosix"; when run on SLURM system, specify "slurm".
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POPULATION: If you use reference file "AFR", define this to AFR. You have 5 optiones: AFR, AMR, ASN, EUR and SAN.
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GREGOR can run on local machine or on the cluster with MOSIX or SLURM.
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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"
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== Reference Files  ==
 
== Reference Files  ==
 
We provide two kinds of reference files. The difference between these reference data are LD buddy definitions.
 
We provide two kinds of reference files. The difference between these reference data are LD buddy definitions.
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LD window size = 1MB; LD r2 ≥ 0.7：
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*LD window size = 1MB; LD r2 ≥ 0.7：
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    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.
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**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.
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LD window size = 1MB; LD r2 ≥ 0.2：  
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*LD window size = 1MB; LD r2 ≥ 0.2：  
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    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.
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**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.
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== Results Output ==
 
== Results Output ==
 
The file StatisticSummaryFile.txt in the output directory contains enrichment results with the following information:
 
The file StatisticSummaryFile.txt in the output directory contains enrichment results with the following information:
Jchen
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