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Revision as of 21:38, 23 November 2014
, 21:38, 23 November 2014→GotCloud BAM Index File
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=== 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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<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]]
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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?
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<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>
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<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>
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>
