3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Variant Calling and Filtering for SNPs Practical, June 2014 (view source)
Revision as of 14:37, 13 November 2014
, 14:37, 13 November 2014no edit summary
'''Note:''' the latest version of this practical is available at: [[SeqShop: Variant Calling and Filtering for SNPs Practical]]
* The ones here is the original one from the June workshop (updated to be run from elsewhere)
==Introduction==
==Introduction==
See the [[Media:SeqShop - GotCloud snpcall.pdf|introductory slides]] for an intro to this tutorial.
See the [[Media:SeqShop - GotCloud snpcall.pdf|introductory slides]] for an intro to this tutorial.
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]]
This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, June 2014|Alignment Tutorial]]
{{SeqShopRemoteEnv}}
{{SeqShopRemoteEnv}}
Per sample BAM files contain sequence reads that are mapped to positions in the genome.
Per sample BAM files contain sequence reads that are mapped to positions in the genome.
For a reminder on how to look at/read BAM files, see: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#BAM_Files|SeqShop Aligment: BAM Files]]
For a reminder on how to look at/read BAM files, see: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, June 2014#BAM_Files|SeqShop Aligment: BAM Files]]
For this tutorial, we will use the 4 BAMs produced in the [[SeqShop: Sequence Mapping and Assembly Practical]] as well as with 58 BAMs that were pre-aligned to that 1MB region of chromosome 22.
For this tutorial, we will use the 4 BAMs produced in the [[SeqShop: Sequence Mapping and Assembly Practical, June 2014]] as well as with 58 BAMs that were pre-aligned to that 1MB region of chromosome 22.
=== Reference Files ===
=== Reference Files ===
<li>View Screenshot</li>
<li>View Screenshot</li>
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
[[File:RefDir.png|500px]]
[[File:RefDir.png|700px]]
</div>
</div>
</div>
</div>
;Do you notice a difference between this index and yours?
;Do you notice a difference between this index and yours?
<ul>
<ul>
<div class="mw-collapsible mw-collapsed" style="width:500px">
<div class="mw-collapsible mw-collapsed" style="width:550px">
<li>Answer:</li>
<li>Answer:</li>
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
<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 index has /home/...</li>
[[File:Bamindex1.png|300px]]
[[File:Bamindex1.png|300px]]
<li>That's ok, <code>gotcloud.conf</code> contains the path to those BAMs</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
<pre>BAM_INDEX = /home/username/seqshop/example</pre> </li>
<ul>
<li>NOTE: the conf file can't interpret ${SS} environment variables or '~', so you would have to specify the full path</li>
<li>We just used the command-line option for this tutorial since this path will vary by user.</li>
</ul>
</div>
</div>
</div>
</div>
We need to add these BAMs to our index
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
* Append the bam.index from the pre-aligned BAMs to the one you generated from the alignment pipeline
** '''Be sure to do this command just once'''
cat ${SS}/bams/bam.index >> ${OUT}/bam.index
cat ${SS}/bams/bam.index >> ${OUT}/bam.index
* ">>" 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 index is the correct size
**:<pre>wc -l ${OUT}/bam.index</pre>
**:<pre>wc -l ${OUT}/bam.index</pre>
We will use the same configuration file as we used yesterday in GotCloud Align.
We will use the same configuration file as we used yesterday in GotCloud Align.
See [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#GotCloud Configuration File|SeqShop: Alignment: GotCloud Configuration File]] for more details
See [[SeqShop:_Sequence Mapping and Assembly Practical, June 2014#GotCloud Configuration File|SeqShop: Alignment: GotCloud Configuration File]] for more details
* Note we want to limit snpcall to just chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X).
* Note we want to limit snpcall to just chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X).
; What's new in the output directory?
; What's new in the output directory?
<ul>
<ul>
<div class="mw-collapsible mw-collapsed" style="width:500px">
<div class="mw-collapsible mw-collapsed" style="width:500px">
<li>Answer</li>
<li>Answer</li>
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
:<pre>ls ${OUT}</pre>
<ul>
<ul>
<li><code>beagle</code> directory : Beagle output</li>
<li><code>beagle</code> directory : Beagle output</li>
</ul>
</ul>
Let's take a look at that interesting location we found in the [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#Accessing_BAMs_by_Position|alignment tutorial]] : chromosome 22, positions 36907000-36907100
Let's take a look at that interesting location we found in the [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, June 2014#Accessing_BAMs_by_Position|alignment tutorial]] : chromosome 22, positions 36907000-36907100
Use tabix to extract that from the VCFs:
Use tabix to extract that from the VCFs:
