Difference between revisions of "Test EPACTS for DIAGRAM"

From Genome Analysis Wiki
Jump to navigationJump to search
 
(35 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
= Download  EPACTS =
+
= Download EPACTS =
  
−
EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/epacts_v2_01.noref_binary.2012_07_06.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  
  
−
*Linux 64bit
+
*Linux 64bit  
−
*Perl vX
+
*Perl 5
−
*gcc vX
 
  
−
= Install EPACTS =
+
= Install EPACTS =
  
−
Uncompress EPACTS package to the directory you would like to install
+
Uncompress EPACTS package to the directory you would like to install  
−
  tar xzvf epacts_v2_01.noref_binary.2012_07_06.tar.gz
+
<pre> tar xzvf epacts_v2_12.noref_binary.2012_10_01.tar.gz</pre>
 +
Download the reference FASTA files from 1000 Genomes FTP automatically by running the following commands<br>
 +
<pre>cd epacts2.1/
 +
./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>
 +
 
 +
= Accessing help  =
 +
 
 +
For a list of commands available in EPACTS, type in the following commands:
 +
<pre>$ epacts2.1/epacts help
 +
 
 +
Usage:
 +
epacts [command] [options]
 +
 
 +
Command:
 +
help Print out brief help message
 +
man Print the full documentation in man page style
 +
single Perform single variant association
 +
group Perform groupwise (burden-style) association test
 +
anno Annotate a VCF file
 +
zoom Create a locus zoom plot from epacts results
 +
meta Perform meta-analysis across multiple epacts results
 +
make-group Create the group information for gene-based testing
 +
make-kin Create a kinship matrix
 +
 
 +
Visit http://genome.sph.umich.edu/wiki/EPACTS for more detailed documentation
 +
 
 +
</pre>
 +
 
 +
 
 +
To view options for single variant testing only type in:
 +
<pre>$ epacts2.1/epacts single -help
 +
Usage:
 +
epacts single [options]
 +
 
 +
Required Options (Run epacts single -man or see wiki for more info):
 +
-vcf STR Input VCF file (tabixed and bgzipped)
 +
-ped STR Input PED file for phenotypes and covariates
 +
-out STR Prefix of output files
 +
-test STR Statistical test to use
 +
...
 +
</pre>
 +
 
 +
= Getting started in EPACTS with an example  =
  
−
= Example =
 
 
Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are:  
 
Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are:  
−
<pre>${EPACTS_DIRECTORY}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
+
<pre>$ epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
  
−
${EPACTS_DIRECTORY}/example/1000G_dummy_pheno.ped
+
$ epacts2.1/example/1000G_dummy_pheno.ped
 
</pre>  
 
</pre>  
 
<br> Run the single variant score test on the example data using this command:  
 
<br> Run the single variant score test on the example data using this command:  
−
<pre>${EPACTS_DIR}/epacts single \
+
<pre>$ epacts2.1/epacts single \
−
--vcf {EPACTS_DIR}/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
+
--vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
−
--ped {EPACTS_DIR}/example/1000G_dummy_pheno.ped \
+
--ped epacts2.1/example/1000G_dummy_pheno.ped \
 
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \
 
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \
 
--out {OUTPUT_DIR}/test --run 2 &amp;
 
--out {OUTPUT_DIR}/test --run 2 &amp;
 
</pre>  
 
</pre>  
 +
This command will run the '''single '''variant test on the input '''VCF '''and '''PED '''files, with a '''minimum MAF''' threshold of 0.001. &nbsp;The '''phenotype '''is "DISEASE" and we are adjusting the analysis with '''covariates '''AGE and SEX. &nbsp;The '''output file directory prefix''' is {OUTPUT_DIR}/test. &nbsp;Finally, EPACTS will run the analysis '''in parallel on 2 CPUs'''.
 +
 +
== Expected output  ==
 +
 +
EPACTS produces a number of files and plots.
 +
 +
1. &nbsp;'''test.epacts.gz'''&nbsp;contains all the association results.
 +
<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
 +
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      NA      NA      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      NA      NA      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      NA      NA      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      NA      NA      NA      NA
 +
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>
 +
The columns in the results file are:
 +
 +
#CHROM: &nbsp;chromosome
 +
#BEGIN: &nbsp;starting position
 +
#END: ending position (same as BEGIN if a SNP)
 +
#MARKER_ID: &nbsp;name of varian
 +
#NS: &nbsp;Number of samples (cases + controls)
 +
#AC: &nbsp;Total allele count in sample
 +
#CALLRATE: &nbsp;call rate
 +
#MAF: &nbsp;minor allele frequency in full sample
 +
#PVALUE: &nbsp;score test association p-value
 +
#SCORE: &nbsp;test statistic for score test
 +
#N.CASE: &nbsp;number of cases
 +
#N.CTRL: &nbsp;number of controls
 +
#AF.CASE: &nbsp;allele frequency in cases only
 +
#AF.CTRL: &nbsp;allele frequency in controls only
 +
 +
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").
 +
 +
<br>
 +
 +
2. &nbsp;'''test.epacts.top5000''' contains the top 5000 associated variants ordered by p-value.
 +
<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
 +
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 145    121    0.62759 0.93388
 +
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 145    121    0.68276 0.95868
 +
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  145    121    0.44828 0.2562
 +
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  145    121    0.11724 0.024793
 +
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>
 +
3. &nbsp;'''test.epacts.qq.pdf''' contains the Q-Q plot of test p-values (stratified by MAF)<br>[[Image:Test b score epacts qq.png]]
 +
 +
4. &nbsp;'''test.epacts.mh.pdf''' contains the Manhattan Plot of test p-values<br>The file out/test.b.score.epacts.mh.pdf will be generated for chr20 only.
 +
 +
[[Image:Test b score epacts mh.png]]
  
−
This command will run the single variant test on the input VCF and PED files, with a minimum MAF threshold of 0.001. &nbsp;The phenotype is "DISEASE" and we are adjusting the analysis with covariates AGE and SEX. &nbsp;The output file directory prefix is {OUTPUT_DIR}/test. &nbsp;Finally, EPACTS will run the analysis in parallel on 2 CPUs.
+
An example Genome-wide manhattan plot (from a genome-wide run) will look like below<br><br> [[Image:Tes b score epacts mh gw.png]] <br>

Latest revision as of 10:28, 2 February 2017

Download EPACTS

EPACTS is available for download here (100Mb) .

Requirements

  • Linux 64bit
  • Perl 5

Install EPACTS

Uncompress EPACTS package to the directory you would like to install 

 tar xzvf epacts_v2_12.noref_binary.2012_10_01.tar.gz

Download the reference FASTA files from 1000 Genomes FTP automatically by running the following commands

cd epacts2.1/
./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/)

Accessing help

For a list of commands available in EPACTS, type in the following commands: 

$ epacts2.1/epacts help

Usage:
epacts [command] [options]

Command:
help Print out brief help message
man Print the full documentation in man page style
single Perform single variant association
group Perform groupwise (burden-style) association test
anno Annotate a VCF file
zoom Create a locus zoom plot from epacts results
meta Perform meta-analysis across multiple epacts results
make-group Create the group information for gene-based testing
make-kin Create a kinship matrix

Visit http://genome.sph.umich.edu/wiki/EPACTS for more detailed documentation


To view options for single variant testing only type in: 

$ epacts2.1/epacts single -help
Usage:
epacts single [options]

Required Options (Run epacts single -man or see wiki for more info):
-vcf STR Input VCF file (tabixed and bgzipped)
-ped STR Input PED file for phenotypes and covariates
-out STR Prefix of output files
-test STR Statistical test to use
...

Getting started in EPACTS with an example

Once installed, test out the software by running a quick example using the test data provided in the "example" directory. The example VCF and PED files are: 

$ epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz

$ epacts2.1/example/1000G_dummy_pheno.ped


Run the single variant score test on the example data using this command: 

$ epacts2.1/epacts single \
--vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \
--ped epacts2.1/example/1000G_dummy_pheno.ped \
--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \
--out {OUTPUT_DIR}/test --run 2 &

This command will run the single variant test on the input VCF and PED files, with a minimum MAF threshold of 0.001.  The phenotype is "DISEASE" and we are adjusting the analysis with covariates AGE and SEX.  The output file directory prefix is {OUTPUT_DIR}/test.  Finally, EPACTS will run the analysis in parallel on 2 CPUs.

Expected output

EPACTS produces a number of files and plots.

1.  test.epacts.gz contains all the association results. 

$ head {OUTPUT_DIR}/test.epacts
#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      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      NA      NA      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      NA      NA      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      NA      NA      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 145     121     0.013793        0.0082645

The columns in the results file are:

  1. CHROM:  chromosome
  2. BEGIN:  starting position
  3. END: ending position (same as BEGIN if a SNP)
  4. MARKER_ID:  name of varian
  5. NS:  Number of samples (cases + controls)
  6. AC:  Total allele count in sample
  7. CALLRATE:  call rate
  8. MAF:  minor allele frequency in full sample
  9. PVALUE:  score test association p-value
  10. SCORE:  test statistic for score test
  11. N.CASE:  number of cases
  12. N.CTRL:  number of controls
  13. AF.CASE:  allele frequency in cases only
  14. 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").


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

$ 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
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 145     121     0.62759 0.93388
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 145     121     0.68276 0.95868
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  145     121     0.44828 0.2562
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  145     121     0.11724 0.024793
20      34288854        34288854        20:34288854_C/T_Utr3:ROMO1      266     28      1       0.052632        0.0047722       2.822   145     121     0.15862 0.041322

3.  test.epacts.qq.pdf contains the Q-Q plot of test p-values (stratified by MAF)
Test b score epacts qq.png

4.  test.epacts.mh.pdf contains the Manhattan Plot of test p-values
The file out/test.b.score.epacts.mh.pdf will be generated for chr20 only.

Test b score epacts mh.png

An example Genome-wide manhattan plot (from a genome-wide run) will look like below

Tes b score epacts mh gw.png

Retrieved from "http://genome.sph.umich.edu/w/index.php?title=Test_EPACTS_for_DIAGRAM&oldid=14588"