Test EPACTS for DIAGRAM - Revision history

Ppwhite: /* Download EPACTS */

2017-02-02T14:28:32Z

Download EPACTS

← Older revision		Revision as of 10:28, 2 February 2017
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	= Download EPACTS =		= Download EPACTS =

	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) ].		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

Clement Ma at 15:26, 5 October 2012

2012-10-05T15:26:01Z

← Older revision		Revision as of 11:26, 5 October 2012
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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
	<pre> tar xzvf epacts_v2_12.noref_binary.2012_10_01.tar.gz</pre>		<pre> tar xzvf epacts_v2_12.noref_binary.2012_10_01.tar.gz</pre>
	~~<br>~~Download the reference FASTA files by running the following commands		Download the reference FASTA files from 1000 Genomes FTP automatically by running the following commands<br>
	<pre>cd epacts2.1/		<pre>cd epacts2.1/
	./ref_download.sh (Or copy ~~the~~ FASTA and index file ~~locally you have~~ to ${EPACTS_DIR}/ext/ref/)		./ref_download.sh
			(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>

Clement Ma: /* Expected output */

2012-10-04T18:59:58Z

Expected output

← Older revision		Revision as of 14:59, 4 October 2012
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	</pre>		</pre>
			The columns in the results file are:

			#CHROM:  chromosome
			#BEGIN:  starting position
			#END: ending position (same as BEGIN if a SNP)
			#MARKER_ID:  name of varian
			#NS:  Number of samples (cases + controls)
			#AC:  Total allele count in sample
			#CALLRATE:  call rate
			#MAF:  minor allele frequency in full sample
			#PVALUE:  score test association p-value
			#SCORE:  test statistic for score test
			#N.CASE:  number of cases
			#N.CTRL:  number of controls
			#AF.CASE:  allele frequency in cases only
			#AF.CTRL:  allele frequency in controls only

	Note:  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").		Note:  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").

Clement Ma at 02:51, 3 October 2012

2012-10-03T02:51:28Z

← Older revision		Revision as of 22:51, 2 October 2012
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	</pre>		</pre>
	Note:  For variants ~~that do not meet~~ the minimum MAF threshold (~~MAF >~~= 0.001), the number of cases and controls (N.CASE, N.CTRL) are not outputted (listed as "NA").		Note:  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").


			<br>

	2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.		2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.

Clement Ma: /* Expected output */

2012-10-03T02:50:50Z

Expected output

← Older revision		Revision as of 22:50, 2 October 2012
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	</pre>		</pre>
			Note:  For variants that do not meet the minimum MAF threshold (MAF >= 0.001), the number of cases and controls (N.CASE, N.CTRL) are not outputted (listed as "NA").



	2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.		2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
	<pre>$ head {OUTPUT_DIR}/test.epacts.top5000		<pre>$ head {OUTPUT_DIR}/test.epacts.top5000

Clement Ma at 21:21, 1 October 2012

2012-10-01T21:21:06Z

← Older revision		Revision as of 17:21, 1 October 2012
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	1.  '''test.epacts.gz''' contains all the association results.		1.  '''test.epacts.gz''' contains all the association results.
	<pre>$ head {OUTPUT_DIR}/test~~.single.b.score~~.epacts		<pre>$ head {OUTPUT_DIR}/test.epacts
	#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE N.CASE N.CTRL AF.CASE AF.CTRL		#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE N.CASE N.CTRL AF.CASE AF.CTRL
	20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA NA NA NA NA		20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA NA NA NA NA
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	</pre>		</pre>
	2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.		2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
	<pre>$ head {OUTPUT_DIR}/test~~.single.b.score~~.epacts.top5000		<pre>$ head {OUTPUT_DIR}/test.epacts.top5000
	#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE N.CASE N.CTRL AF.CASE AF.CTRL		#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE N.CASE N.CTRL AF.CASE AF.CTRL
	20 1610894 1610894 20:1610894_G/A_Synonymous:SIRPG 266 136 1 0.25564 0.0001097 3.8681 145 121 0.64138 0.35537		20 1610894 1610894 20:1610894_G/A_Synonymous:SIRPG 266 136 1 0.25564 0.0001097 3.8681 145 121 0.64138 0.35537

Clement Ma: /* Expected output */

2012-10-01T21:20:42Z

Expected output

Clement Ma: /* Install EPACTS */

2012-10-01T21:09:26Z

Install EPACTS

← Older revision		Revision as of 17:09, 1 October 2012
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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
	<pre> tar xzvf ~~epacts_v2_01~~.noref_binary.~~2012_09_27~~.tar.gz</pre>		<pre> tar xzvf epacts_v2_12.noref_binary.2012_10_01.tar.gz</pre>
	<br>Download the reference FASTA files by running the following commands		<br>Download the reference FASTA files by running the following commands
	<pre>cd epacts2.1/		<pre>cd epacts2.1/

Clement Ma: /* Download EPACTS */

2012-10-01T21:05:36Z

Download EPACTS

← Older revision		Revision as of 17:05, 1 October 2012
Line 1:		Line 1:
	= Download EPACTS =		= Download EPACTS =

	EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/epacts_v2.1.noref_binary.~~2012_09_27~~.tar.gz here (100Mb) ].		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) ].

	Requirements		Requirements

Clement Ma at 14:49, 28 September 2012

2012-09-28T14:49:31Z

← Older revision		Revision as of 10:49, 28 September 2012
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	1.  '''test.epacts.gz''' contains all the association results.		1.  '''test.epacts.gz''' contains all the association results.
	<pre>$ head test.epacts		<pre>$ head {OUTPUT_DIR}/test.epacts
	#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE		#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE
	20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA		20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA
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	</pre>		</pre>
	2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.		2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
	<pre>$ head ~~out~~/test.single.b.score.epacts.top5000		<pre>$ head {OUTPUT_DIR}/test.single.b.score.epacts.top5000
	#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE		#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE
	20 1610894 1610894 20:1610894_G/A_Synonymous:SIRPG 266 136 1 0.25564 0.0001097 3.8681		20 1610894 1610894 20:1610894_G/A_Synonymous:SIRPG 266 136 1 0.25564 0.0001097 3.8681

← Older revision		Revision as of 17:20, 1 October 2012
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	1.  '''test.epacts.gz''' contains all the association results.		1.  '''test.epacts.gz''' contains all the association results.
	<pre>$ head {OUTPUT_DIR}/test.epacts		<pre>$ head {OUTPUT_DIR}/test.single.b.score.epacts
	#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE		#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE N.CASE N.CTRL AF.CASE AF.CTRL
	20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA		20 68303 68303 20:68303_A/G_Upstream:DEFB125 266 1 1 0.0018797 NA NA NA NA NA NA
	20 68319 68319 20:68319_C/A_Upstream:DEFB125 266 0 1 0 NA NA		20 68319 68319 20:68319_C/A_Upstream:DEFB125 266 0 1 0 NA NA NA NA NA NA
	20 68396 68396 20:68396_C/T_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA		20 68396 68396 20:68396_C/T_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA NA NA NA NA
	20 76635 76635 20:76635_A/T_Intron:DEFB125 266 0 1 0 NA NA		20 76635 76635 20:76635_A/T_Intron:DEFB125 266 0 1 0 NA NA NA NA NA NA
	20 76689 76689 20:76689_T/C_Synonymous:DEFB125 266 0 1 0 NA NA		20 76689 76689 20:76689_T/C_Synonymous:DEFB125 266 0 1 0 NA NA NA NA NA NA
	20 76690 76690 20:76690_T/C_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA		20 76690 76690 20:76690_T/C_Nonsynonymous:DEFB125 266 1 1 0.0018797 NA NA NA NA NA NA
	20 76700 76700 20:76700_G/A_Nonsynonymous:DEFB125 266 0 1 0 NA NA		20 76700 76700 20:76700_G/A_Nonsynonymous:DEFB125 266 0 1 0 NA NA NA NA NA NA
	20 76726 76726 20:76726_C/G_Nonsynonymous:DEFB125 266 0 1 0 NA NA		20 76726 76726 20:76726_C/G_Nonsynonymous:DEFB125 266 0 1 0 NA NA NA NA NA NA
	20 76771 76771 20:76771_C/T_Nonsynonymous:DEFB125 266 3 1 0.0056391 0.68484 0.40587		20 76771 76771 20:76771_C/T_Nonsynonymous:DEFB125 266 3 1 0.0056391 0.68484 0.40587 145 121 0.013793 0.0082645

	</pre>		</pre>
	2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.		2.  '''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
	<pre>$ head {OUTPUT_DIR}/test.single.b.score.epacts.top5000		<pre>$ head {OUTPUT_DIR}/test.single.b.score.epacts.top5000
	#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE		#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE N.CASE N.CTRL AF.CASE AF.CTRL
	20 1610894 1610894 20:1610894_G/A_Synonymous:SIRPG 266 136 1 0.25564 0.0001097 3.8681		20 1610894 1610894 20:1610894_G/A_Synonymous:SIRPG 266 136 1 0.25564 0.0001097 3.8681 145 121 0.64138 0.35537
	20 4162411 4162411 20:4162411_T/C_Intron:SMOX 266 204 1 0.38346 0.00055585 -3.4523		20 4162411 4162411 20:4162411_T/C_Intron:SMOX 266 204 1 0.38346 0.00055585 -3.4523 145 121 0.62759 0.93388
	20 34061918 34061918 20:34061918_T/C_Intron:CEP250 266 39 1 0.073308 0.0011231 3.2577		20 34061918 34061918 20:34061918_T/C_Intron:CEP250 266 39 1 0.073308 0.0011231 3.2577 145 121 0.21379 0.066116
	20 4155948 4155948 20:4155948_G/A_Intron:SMOX 266 215 1 0.40414 0.0020791 -3.0787		20 4155948 4155948 20:4155948_G/A_Intron:SMOX 266 215 1 0.40414 0.0020791 -3.0787 145 121 0.68276 0.95868
	20 4680251 4680251 20:4680251_A/G_Nonsynonymous:PRNP 266 186 1 0.34962 0.0025962 3.0119		20 4680251 4680251 20:4680251_A/G_Nonsynonymous:PRNP 266 186 1 0.34962 0.0025962 3.0119 145 121 0.8069 0.57025
	20 36668874 36668874 20:36668874_G/A_Synonymous:RPRD1B 266 96 1 0.18045 0.003031 2.9646		20 36668874 36668874 20:36668874_G/A_Synonymous:RPRD1B 266 96 1 0.18045 0.003031 2.9646 145 121 0.44828 0.2562
	20 36641871 36641871 20:36641871_G/A_Synonymous:TTI1 266 10 1 0.018797 0.004308 -2.8547		20 36641871 36641871 20:36641871_G/A_Synonymous:TTI1 266 10 1 0.018797 0.004308 -2.8547 145 121 0.0068966 0.07438
	20 32664926 32664926 20:32664926_G/A_Nonsynonymous:RALY 266 20 1 0.037594 0.0046365 2.8313		20 32664926 32664926 20:32664926_G/A_Nonsynonymous:RALY 266 20 1 0.037594 0.0046365 2.8313 145 121 0.11724 0.024793
	20 34288854 34288854 20:34288854_C/T_Utr3:ROMO1 266 28 1 0.052632 0.0047722 2.822		20 34288854 34288854 20:34288854_C/T_Utr3:ROMO1 266 28 1 0.052632 0.0047722 2.822 145 121 0.15862 0.041322

	</pre>		</pre>
	3.  '''test.epacts.qq.pdf''' contains the Q-Q plot of test p-values (stratified by MAF)<br>[[Image:Test b score epacts qq.png]]		3.  '''test.epacts.qq.pdf''' contains the Q-Q plot of test p-values (stratified by MAF)<br>[[Image:Test b score epacts qq.png]]