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Test EPACTS for DIAGRAM (view source)

Revision as of 10:28, 2 February 2017

712 bytes added ,  10:28, 2 February 2017
→‎Download EPACTS
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= Download EPACTS  =
 
= Download EPACTS  =
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EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/epacts_v2.12.noref_binary.2012_10_01.tar.gz here (100Mb) ].  
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EPACTS is available for download [http://csg.sph.umich.edu//kang/epacts/download/epacts_v2.12.noref_binary.2012_10_01.tar.gz here (100Mb) ].  
    
Requirements  
 
Requirements  
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Uncompress EPACTS package to the directory you would like to install  
 
Uncompress EPACTS package to the directory you would like to install  
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<pre> tar xzvf epacts_v2_12.noref_binary.2012_10_01.tar.gz</pre>
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<pre> tar xzvf epacts_v2_12.noref_binary.2012_10_01.tar.gz</pre>  
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<br>Download the reference FASTA files by running the following commands
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Download the reference FASTA files from 1000 Genomes FTP automatically by running the following commands<br>
 
<pre>cd epacts2.1/
 
<pre>cd epacts2.1/
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./ref_download.sh (Or copy the FASTA and index file locally you have to ${EPACTS_DIR}/ext/ref/)
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./ref_download.sh
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(For advanced users, to save time for downloading the FASTA files (~900MB), you may copy a local copy of GRCh37 FASTA file and the index file to ${EPACTS_DIR}/ext/ref/)
 
</pre>
 
</pre>
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</pre>  
 
</pre>  
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Note: &nbsp;For variants that do not meet the minimum MAF threshold (MAF &gt;= 0.001), the number of cases and controls (N.CASE, N.CTRL) are not outputted (listed as "NA").
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The columns in the results file are:
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#CHROM: &nbsp;chromosome
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#BEGIN: &nbsp;starting position
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#END: ending position (same as BEGIN if a SNP)
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#MARKER_ID: &nbsp;name of varian
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#NS: &nbsp;Number of samples (cases + controls)
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#AC: &nbsp;Total allele count in sample
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#CALLRATE: &nbsp;call rate
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#MAF: &nbsp;minor allele frequency in full sample
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#PVALUE: &nbsp;score test association p-value
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#SCORE: &nbsp;test statistic for score test
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#N.CASE: &nbsp;number of cases
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#N.CTRL: &nbsp;number of controls
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#AF.CASE: &nbsp;allele frequency in cases only
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#AF.CTRL: &nbsp;allele frequency in controls only
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Note: &nbsp;For variants below the minimum MAF threshold (min-maf = 0.001), the number of cases and controls (N.CASE, N.CTRL) are not outputted (listed as "NA").
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<br>
    
2. &nbsp;'''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.  
 
2. &nbsp;'''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.  
Ppwhite
96

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