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SeqShop: Genetic Association Analysis Practical, December 2014 (view source)

Revision as of 10:27, 2 February 2017

1,943 bytes added ,  10:27, 2 February 2017
→‎Download & Build EPACTS
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== Introduction ==
 
== Introduction ==
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Main Workshop wiki page: [[SeqShop: May 2015]]
 +
 
[[Media:Seqshop association 2014 06.pdf|View Lecture Slides]]
 
[[Media:Seqshop association 2014 06.pdf|View Lecture Slides]]
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== Setup in person at the SeqShop Workshop ==
 
== Setup in person at the SeqShop Workshop ==
 
''This section is specifically for the SeqShop Workshop computers.''
 
''This section is specifically for the SeqShop Workshop computers.''
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<div class="mw-collapsible" style="width:600px">
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<div class="mw-collapsible mw-collapsed" style="width:600px">
 
''If you are not running during the SeqShop Workshop, please skip this section.''
 
''If you are not running during the SeqShop Workshop, please skip this section.''
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
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== Setup when running on your own outside of the SeqShop Workshop ==
 
== Setup when running on your own outside of the SeqShop Workshop ==
 
''This section is specifically for running on your own outside of the SeqShop Workshop.''
 
''This section is specifically for running on your own outside of the SeqShop Workshop.''
−
<div class="mw-collapsible mw-collapsed" style="width:600px">
+
<div class="mw-collapsible" style="width:600px">
 
''If you are running during the SeqShop Workshop, please skip this section.''
 
''If you are running during the SeqShop Workshop, please skip this section.''
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
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  cd ~/seqshop/
 
  cd ~/seqshop/
 
* download, decompress, and build the version of epacts that was tested with this tutorial:
 
* download, decompress, and build the version of epacts that was tested with this tutorial:
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  wget http://www.sph.umich.edu/csg/kang/epacts/download/EPACTS-3.2.6.tar.gz
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  wget http://csg.sph.umich.edu//kang/epacts/download/EPACTS-3.2.6.tar.gz
 
  tar xvf EPACTS-3.2.6.tar.gz
 
  tar xvf EPACTS-3.2.6.tar.gz
 
  cd EPACTS-3.2.6
 
  cd EPACTS-3.2.6
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Let's run a single-variant association analysis using a score test.  
 
Let's run a single-variant association analysis using a score test.  
   −
  $EPACTS/bin/epacts-single --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/single --region 22:36000000-37000000 --test b.score --pheno PHENO --run 2  
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  $EPACTS/bin/epacts single --ped $SS/assoc/seqshop.ped --vcf $OUT/assoc/snps.anno.vcf.gz --out $OUT/assoc/single --region 22:36000000-37000000 --test b.score --min-mac 1 --pheno PHENO --run 2
    
After running it, you will see EPACTS output files by looking at
 
After running it, you will see EPACTS output files by looking at
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  22 36987861 36987861 22:36987861_A/G 62 31 1 0.25 2.0898e-06 4.7445 31 31 0.43548 0.064516
 
  22 36987861 36987861 22:36987861_A/G 62 31 1 0.25 2.0898e-06 4.7445 31 31 0.43548 0.064516
 
  22 36985499 36985499 22:36985499_C/T 62 29 1 0.23387 5.7389e-06 4.5358 31 31 0.40323 0.064516
 
  22 36985499 36985499 22:36985499_C/T 62 29 1 0.23387 5.7389e-06 4.5358 31 31 0.40323 0.064516
 +
22 36998907 36998907 22:36998907_C/T 62 58 1 0.46774 1.3679e-05 -4.3489 31 31 0.25806 0.67742
 
  22 36978260 36978260 22:36978260_G/T 62 28 1 0.22581 1.5051e-05 4.3279 31 31 0.3871 0.064516
 
  22 36978260 36978260 22:36978260_G/T 62 28 1 0.22581 1.5051e-05 4.3279 31 31 0.3871 0.064516
−
  22 36998907 36998907 22:36998907_C/T 62 61 1 0.49194 0.00015557 -3.782 31 31 0.30645 0.67742
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  22 36667082 36667082 22:36667082_T/G 62 27 1 0.21774 0.00015573 -3.7817 31 31 0.064516 0.37097
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  22 36667082 36667082 22:36667082_T/G 62 28 1 0.22581 0.0003506 -3.5747 31 31 0.080645 0.37097
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</div>
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</div>
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<div class="mw-collapsible mw-collapsed" style="width:400px">
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Interpretation for top associated variant chr22:36995620_A/G:
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<div class="mw-collapsible-content" style="width:800px">
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#CHROM BEGIN END MARKER_ID NS AC CALLRATE MAF PVALUE SCORE NS.CASE NS.CTRL AF.CASE AF.CTRL
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  22 36995620 36995620 22:36995620_A/G 62 36 1 0.29032 5.6717e-09 5.8262 31 31 0.51613 0.064516
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 +
The score test PVALUE = 5.6717e-09 is strongly significant.
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For the notation chr22:36995620_A/G, the reference allele is the first allele "A", and the non-reference (effect) allele is the second allele "G".
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The SCORE statistic = 0.29032 is positive (e.g. SCORE>0), meaning that the effect allele INCREASES your risk for disease.  Note that the SCORE is NOT the BETA or log odds ratio.  To calculate the BETA and SE(BETA), you must run the b.wald test.
 +
There is a large difference between the allele frequencies for cases and controls.  AF.CASE = 0.51613 >> AF.CTRL = 0.0064516.
 
</div>
 
</div>
 
</div>
 
</div>
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The group file is simply a list of marker per group name, as shown below.
 
The group file is simply a list of marker per group name, as shown below.
   −
  cat $OUT/assoc/snps.anno.grp  
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  cat $OUT/assoc/snps.anno.grp
 +
 
 
  APOL1 22:36655735_G/A 22:36657740_G/A 22:36661330_G/A 22:36661566_G/A 22:36661646_G/A 22:36661891_G/A 22:36661906_A/G
 
  APOL1 22:36655735_G/A 22:36657740_G/A 22:36661330_G/A 22:36661566_G/A 22:36661646_G/A 22:36661891_G/A 22:36661906_A/G
 
  APOL2 22:36623731_T/C 22:36623920_G/A 22:36629466_T/A 22:36633107_C/A
 
  APOL2 22:36623731_T/C 22:36623920_G/A 22:36629466_T/A 22:36633107_C/A
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View Output file
 
View Output file
 
<div class="mw-collapsible-content" style="width:800px">
 
<div class="mw-collapsible-content" style="width:800px">
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  #CHROM BEGIN END MARKER_ID NS FRAC_WITH_RARE NUM_ALL_VARS NUM_PASS_VARS NUM_SING_VARS PVALUE STATRHO
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  #CHROM BEGIN   END     MARKER_ID       NS     FRAC_WITH_RARE NUM_ALL_VARS   NUM_PASS_VARS   NUM_SING_VARS   PVALUE BETA    SEBETA  ZSTAT
−
  22 36655735 36661906 22:36655735-36661906_APOL1 62 0.14516 7 4 0 0.42748 1
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  22     36655735       36661906       22:36655735-36661906_APOL1     62     0.14516 7       4       0       0.28783 0.80648 0.75876 1.0629
−
  22 36623731 36633107 22:36623731-36633107_APOL2 62 0.064516 4 1 0 0.038657 NA
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  22     36623731       36633107       22:36623731-36633107_APOL2     62     0.064516       4       1       0       0.99286 -17.704 1978.1  -0.0089502
−
  22 36537763 36556823 22:36537763-36556823_APOL3 62 0.080645 4 2 0 0.40634 0
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  22     36537763       36556823       22:36537763-36556823_APOL3     62     0.080645       4       2       0       0.643  -0.44056        0.95048 -0.46351
−
  22 36587154 36598081 22:36587154-36598081_APOL4 62 0.14516 12 4 0 0.67891 0
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  22     36587154       36598081       22:36587154-36598081_APOL4     62     0.096774        12     4       0      0.3989  0.76461 0.90638 0.84358
−
  22 36122356 36124860 22:36122356-36124860_APOL5 62 0.1129 5 2 0 0.15055 0.3
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  22     36122356       36124860       22:36122356-36124860_APOL5     62     0.1129 5       2       0       0.076266        1.9741  1.1136  1.7728
−
  22 36900271 36900806 22:36900271-36900806_FOXRED2 NA NA 2 0 0 NA NA
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  22     36900271       36900806       22:36900271-36900806_FOXRED2   NA     NA     2       0       0       NA      NA      NA     NA
−
  22 36681163 36710183 22:36681163-36710183_MYH9 62 0.032258 3 1 0 1 NA
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  22     36681163       36710183       22:36681163-36710183_MYH9       62     0.048387        3       1       0      0.9904  16.668  1385.4  0.012031
−
  22 36711990 36711990 22:36711990-36711990_Metazoa_SRP NA NA 1 0 0 NA NA
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  22     36711990       36711990       22:36711990-36711990_Metazoa_SRP       NA     NA     1       0       0       NA     NA      NA      NA
−
  22 36424450 36424450 22:36424450-36424450_RBFOX2 62 0.032258 1 1 0 1 NA
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  22     36424450       36424450       22:36424450-36424450_RBFOX2     62     0.032258       1       1       0       1       5.9095e-16      1.4376  4.1107e-16
−
  22 36792162 36792162 22:36792162-36792162_RP4-633O19__A.1 NA NA 1 0 0 NA NA
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  22     36792162       36792162       22:36792162-36792162_RP4-633O19__A.1   NA     NA     1       0       0       NA      NA      NA     NA
 
</div>
 
</div>
 
</div>
 
</div>
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<div class="mw-collapsible-content" style="width:800px">
 
<div class="mw-collapsible-content" style="width:800px">
 
  #CHROM BEGIN END MARKER_ID NS FRAC_WITH_RARE NUM_ALL_VARS NUM_PASS_VARS NUM_SING_VARS PVALUE STATRHO
 
  #CHROM BEGIN END MARKER_ID NS FRAC_WITH_RARE NUM_ALL_VARS NUM_PASS_VARS NUM_SING_VARS PVALUE STATRHO
−
  22 36655735 36661906 22:36655735-36661906_APOL1 62 0.14516 7 4 0 0.42748 1
+
  22 36655735 36661906 22:36655735-36661906_APOL1 62 0.14516 7 4 0 0.22427 1
 
  22 36623731 36633107 22:36623731-36633107_APOL2 62 0.064516 4 1 0 0.038657 NA
 
  22 36623731 36633107 22:36623731-36633107_APOL2 62 0.064516 4 1 0 0.038657 NA
−
  22 36537763 36556823 22:36537763-36556823_APOL3 62 0.080645 4 2 0 0.40634 0
+
  22 36537763 36556823 22:36537763-36556823_APOL3 62 0.080645 4 2 0 0.40763 0
−
  22 36587154 36598081 22:36587154-36598081_APOL4 62 0.14516 12 4 0 0.67891 0
+
  22 36587154 36598081 22:36587154-36598081_APOL4 62 0.096774 12 4 0 0.55686 1
−
  22 36122356 36124860 22:36122356-36124860_APOL5 62 0.1129 5 2 0 0.15055 0.3
+
  22 36122356 36124860 22:36122356-36124860_APOL5 62 0.1129 5 2 0 0.15235 0.3
 
  22 36900271 36900806 22:36900271-36900806_FOXRED2 NA NA 2 0 0 NA NA
 
  22 36900271 36900806 22:36900271-36900806_FOXRED2 NA NA 2 0 0 NA NA
−
  22 36681163 36710183 22:36681163-36710183_MYH9 62 0.032258 3 1 0 1 NA
+
  22 36681163 36710183 22:36681163-36710183_MYH9 62 0.048387 3 1 0 0.075809 NA
 
  22 36711990 36711990 22:36711990-36711990_Metazoa_SRP NA NA 1 0 0 NA NA
 
  22 36711990 36711990 22:36711990-36711990_Metazoa_SRP NA NA 1 0 0 NA NA
 
  22 36424450 36424450 22:36424450-36424450_RBFOX2 62 0.032258 1 1 0 1 NA
 
  22 36424450 36424450 22:36424450-36424450_RBFOX2 62 0.032258 1 1 0 1 NA
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</div>
 
</div>
 
</div>
 
</div>
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== Return to Workshop Wiki Page ==
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Return to main workshop wiki page: [[SeqShop: December 2014]]
Ppwhite
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12359...14587"

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