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

Revision as of 10:27, 2 February 2017

12 bytes added ,  10:27, 2 February 2017
→‎Download & Build EPACTS
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== Introduction ==
 
== Introduction ==
 +
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.''
−
<div class="mw-collapsible" style="width:600px">
+
<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
+
  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  
+
  $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
   
</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">
−
#CHROM  BEGIN  END    MARKER_ID      NS      FRAC_WITH_RARE  NUM_ALL_VARS    NUM_PASS_VARS  NUM_SING_VARS  PVALUE  BETA    SEBETA  ZSTAT
+
#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      0.28783 0.80648 0.75876 1.0629
+
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      0.99286 -17.704 1978.1  -0.0089502
+
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      0.643  -0.44056        0.95048 -0.46351
+
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      0.096774        12      4      0      0.3989  0.76461 0.90638 0.84358
+
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      0.076266        1.9741  1.1136  1.7728
+
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      NA      NA
+
22      36900271        36900806        22:36900271-36900806_FOXRED2    NA      NA      2      0      0      NA      NA      NA      NA
−
22      36681163        36710183        22:36681163-36710183_MYH9      62      0.048387        3      1      0      0.9904  16.668  1385.4  0.012031
+
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      NA      NA
+
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      5.9095e-16      1.4376  4.1107e-16
+
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      NA      NA
+
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>
   −
== Return to Ancestry on your own genome==
+
== Return to Workshop Wiki Page ==
−
Let's go see if Ancestry finished: [[SeqShop:_Ancestry_On_Your_Own_Genome,_December_2014#Checking_if_Pileup_finished]]
+
Return to main workshop wiki page: [[SeqShop: December 2014]]
Ppwhite
96

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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12372...14587"

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