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Revision as of 10:27, 2 February 2017
, 10:27, 2 February 2017→Download & Build EPACTS
== Introduction ==
== Introduction ==
Main Workshop wiki page: [[SeqShop: December 2014]]
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]]
== 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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''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.''
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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.''
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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:
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
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 36667082 36667082 22:36667082_T/G 62 27 1 0.21774 0.00015573 -3.7817 31 31 0.064516 0.37097
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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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
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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#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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== Return to Workshop Wiki Page ==
== Return to Workshop Wiki Page ==
Return to main workshop wiki page: [[SeqShop: December 2014]]
Return to main workshop wiki page: [[SeqShop: December 2014]]
