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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: |
− | 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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| 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
| + | 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 | |
| </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 | + | 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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| <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]] |