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Revision as of 00:21, 15 June 2014
, 00:21, 15 June 2014→Examining GotCloud SnpCall Input files
#* 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 ==
