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, 12:17, 15 June 2014
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| Remember, use <code>'q'</code> to exit out of <code>less</code> | | Remember, use <code>'q'</code> to exit out of <code>less</code> |
| q | | q |
| + | |
| + | |
| + | Now, let's look at the filtered file with genotypes. |
| + | less -S ${OUT}/vcfs/chr22/chr22.filtered.vcf.gz |
| + | |
| + | * Scroll down until you find some variants. |
| + | ** Use space bar to jump a full page |
| + | ** Use down arrow to move down one line |
| + | * Scroll right until you should see per sample genotype information |
| + | |
| + | <div class="mw-collapsible mw-collapsed" style="width:250px"> |
| + | * View annotated screenshot: |
| + | <div class="mw-collapsible-content"> |
| + | [[File:SvmFiltGL.png|550px]] |
| + | </div> |
| + | </div> |
| | | |
| == GotCloud Genotype Refinement == | | == GotCloud Genotype Refinement == |
| | | |
| ${GC}/gotcloud ldrefine --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 | | ${GC}/gotcloud ldrefine --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 |