From Genome Analysis Wiki
Jump to navigationJump to search
1,456 bytes added
, 12:00, 15 June 2014
Line 160: |
Line 160: |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| [[File:gcsnpcallOut.png|500px]] | | [[File:gcsnpcallOut.png|500px]] |
| + | </div> |
| + | </div> |
| + | |
| + | Let's look at the vcfs directory: |
| + | ls ${OUT}/vcfs |
| + | Just a <code>chr22</code> directory, so look inside of there: |
| + | ls ${OUT}/vcfs/chr22 |
| + | ;Can you identify the final filtered VCF and the associated summary file? |
| + | <div class="mw-collapsible mw-collapsed" style="width:350px"> |
| + | * Answer & annotated directory listing: |
| + | <div class="mw-collapsible-content"> |
| + | <ul> |
| + | <li>Filtered VCF (SVM & hard filters): chr22.filtered.vcf.gz</li> |
| + | <li>Summary file: chr22.filtered.sites.vcf.summary</li> |
| + | </ul> |
| + | [[File:vcfsout.png|600px]] |
| + | </div> |
| + | </div> |
| + | |
| + | Now, let's look in the split directory for the VCF with just the passing variants: |
| + | ls ${OUT}/split/chr22 |
| + | ;Which file do you think is the one you want? |
| + | <div class="mw-collapsible mw-collapsed" style="width:350px"> |
| + | * Answer: |
| + | <div class="mw-collapsible-content"> |
| + | <ul> |
| + | <li>chr22.filtered.PASS.vcf.gz</li> |
| + | </ul> |
| + | [[File:splitOut.png|600px]] |
| </div> | | </div> |
| </div> | | </div> |
Line 173: |
Line 202: |
| </div> | | </div> |
| </div> | | </div> |
| + | |
| + | |
| + | === Filtered VCF === |
| + | |
| + | Let's look at the filtered sites file. |
| + | less -S ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf |
| + | |
| + | * 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: lots of info fields, but no per sample genotype information |
| + | |
| + | ;What is the first filtered variant that you find? |
| + | <div class="mw-collapsible mw-collapsed" style="width:250px"> |
| + | * Answer: |
| + | <div class="mw-collapsible-content"> |
| + | [[File:SvmFilt.png|550px]] |
| + | </div> |
| + | </div> |
| + | |
| + | Remember, use <code>'q'</code> to exit out of <code>less</code> |
| + | q |
| | | |
| == 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 |