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| </ul> | | </ul> |
| | | |
− | === GotCloud BAM Index File === | + | === GotCloud BAM List File === |
− | The BAM index file points GotCloud to the BAM files | + | The [[GotCloud:_Variant_Calling_Pipeline#BAM_List_File|BAM list file]] points GotCloud to the BAM files |
| * generated by the alignment pipeline | | * generated by the alignment pipeline |
| | | |
− | Look at the BAM index file the alignment pipeline generated | + | Look at the BAM list file the alignment pipeline generated |
| cat ${OUT}/bam.list | | cat ${OUT}/bam.list |
| | | |
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| <ul> | | <ul> |
| <li>/home/YourUserName/out/bams/HG00640.recal.bam</li> | | <li>/home/YourUserName/out/bams/HG00640.recal.bam</li> |
− | [[File:Bamindex.png|500px]] | + | [[File:BamindexNew.png|500px]] |
| </div> | | </div> |
| </div> | | </div> |
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| ls ${SS}/bams | | ls ${SS}/bams |
| | | |
− | Look at the BAM index for those BAMs: | + | Look at the BAM list file for those BAMs: |
− | less ${SS}/bams/bam.index | + | less ${SS}/bams/bam.list |
| | | |
| 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 |
| | | |
− | ;Do you notice a difference between this index and yours? | + | ;Do you notice a difference between this list and yours? |
| <ul> | | <ul> |
| <div class="mw-collapsible mw-collapsed" style="width:550px"> | | <div class="mw-collapsible mw-collapsed" style="width:550px"> |
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| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| <ul> | | <ul> |
− | <li>It doesn't have a full path to the BAM file, while your index has /home/...</li> | + | <li>It doesn't have a full path to the BAM file, while your list has /home/...</li> |
| [[File:Bamindex1.png|300px]] | | [[File:Bamindex1.png|300px]] |
| <li>That's ok, we will use the <code>--base_prefix ${SS}</code> command-line option to prefix the BAM paths</li> | | <li>That's ok, we will use the <code>--base_prefix ${SS}</code> command-line option to prefix the BAM paths</li> |
− | <li>Alternatively, we could have set BAM_INDEX in <code>gotcloud.conf</code> to the path to the BAMs | + | <li>Alternatively, we could have set BAM_PREFIX in <code>gotcloud.conf</code> to the path to the BAMs |
− | <pre>BAM_INDEX = /home/username/seqshop/example</pre> </li> | + | <pre>BAM_PREFIX = /home/username/seqshop/example</pre> </li> |
| <ul> | | <ul> |
| <li>NOTE: the conf file can't interpret ${SS} environment variables or '~', so you would have to specify the full path</li> | | <li>NOTE: the conf file can't interpret ${SS} environment variables or '~', so you would have to specify the full path</li> |
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| | | |
| | | |
− | We need to add these BAMs to our index | + | We need to add these BAMs to our list |
− | * Append the bam.index from the pre-aligned BAMs to the one you generated from the alignment pipeline | + | * Append the bam.list from the pre-aligned BAMs to the one you generated from the alignment pipeline |
| ** '''Be sure to do this command just once''' | | ** '''Be sure to do this command just once''' |
− | cat ${SS}/bams/bam.index >> ${OUT}/bam.index | + | cat ${SS}/bams/bam.list >> ${OUT}/bam.list |
| * ">>" will append to the file that follows it | | * ">>" will append to the file that follows it |
− | ** Check that your BAM index is the correct size | + | ** Check that your BAM list is the correct size |
− | **:<pre>wc -l ${OUT}/bam.index</pre> | + | **:<pre>wc -l ${OUT}/bam.list</pre> |
| *** <code>wc -l</code> counts the number of lines in the file | | *** <code>wc -l</code> counts the number of lines in the file |
| *** Should be 62 | | *** Should be 62 |
| | | |
− | Verify your BAM index contains the additional BAMs | + | Verify your BAM list contains the additional BAMs |
− | less ${OUT}/bam.index | + | less ${OUT}/bam.list |
| | | |
| Remember, use <code>'q'</code> to exit out of <code>less</code> | | Remember, use <code>'q'</code> to exit out of <code>less</code> |