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| #* hapmap - used for sample contamination/sample swap validation | | #* hapmap - used for sample contamination/sample swap validation |
| #* | | #* |
| + | |
| + | |
| + | === GotCloud Configuration File === |
| + | We will use the same configuration file as we used yesterday in GotCloud Align. |
| | | |
| | | |
| === GotCloud BAM Index File === | | === GotCloud BAM Index File === |
| + | The BAM index file points GotCloud to the BAM files |
| + | * Alignment pipeline generates for you |
| + | * Tab delimited |
| + | |
| + | Look at the BAM index file the alignment pipeline generated |
| + | cat ${OUT}/bam.index |
| + | |
| + | ;What is the path to the BAM file for sample HG00640? |
| + | <ul> |
| + | <div class="mw-collapsible mw-collapsed" style="width:200px"> |
| + | <li>Answer:</li> |
| + | <div class="mw-collapsible-content"> |
| + | <ul> |
| + | <li>/home/YourUserName/out/bams/HG00640.recal.bam</li> |
| + | [[File:Bamindex.png|500px]] |
| + | </div> |
| + | </div> |
| + | </ul> |
| + | </ul> |
| + | |
| + | The alignment pipeline only processed 4 samples, but for snpcall, we want to run on 62 samples. |
| + | * The other 58 samples were already aligned: |
| + | ls ${IN}/bams |
| | | |
− | === GotCloud Configuration File === | + | Look at the BAM index for those BAMs: |
− | We will use the same configuration file as we used yesterday in GotCloud Align. | + | less ${IN}/bams/bam.index |
| + | |
| + | Remember, use <code>'q'</code> to exit out of <code>less</code> |
| + | q |
| + | |
| + | ;Do you notice a difference between this index and yours? |
| + | <ul> |
| + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| + | <li>Answer:</li> |
| + | <div class="mw-collapsible-content"> |
| + | <ul> |
| + | <li>It doesn't have a full path to the BAM file, while your index has /home/...</li> |
| + | [[File:Bamindex1.png|300px]] |
| + | <li>That's ok, <code>gotcloud.conf</code> contains the path to those BAMs</li> |
| + | [[File:BamindexConf.png|300px]] |
| + | </div> |
| + | </div> |
| + | </ul> |
| + | </ul> |
| + | |
| + | |
| + | We need to add these BAMs to our index |
| + | * Append the bam.index from the pre-aligned BAMs to the one you generated from the alignment pipeline |
| + | cat ${IN}/bams/bam.index >> ${OUT}/bam.index |
| + | * ">>" will append to the file that follows it |
| + | |
| + | Verify your BAM index contains the additional BAMs |
| + | less ${IN}/bams/bam.index |
| + | |
| + | Remember, use <code>'q'</code> to exit out of <code>less</code> |
| + | q |
| | | |
| + | ;Do you see both sets of BAMs? |
| + | <ul> |
| + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| + | <li>Screenshot:</li> |
| + | <div class="mw-collapsible-content"> |
| + | <ul> |
| + | <li>If not, let me know</li> |
| + | [[File:Bamindex2.png|400px]] |
| + | </div> |
| + | </div> |
| + | </ul> |
| + | </ul> |
| | | |
| == Run GotCloud SnpCall == | | == Run GotCloud SnpCall == |