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Revision as of 11:31, 14 June 2014
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seqshop/gotcloud/gotcloud snpcall --conf seqshop/inputs/gotcloud.conf --numjobs 4 --region 22:36000000-37000000
== Goals of This Session ==
* What we want to learn
** Basic variant call file format (VCF)
** How to generate filtered variant calls for SNPs
** How to evaluate the quality of variant calls
** How to visualize the variant calls to examine the variants at particular genomic positions
== GotCloud SnpCall Pipeline ==
[[File:SnpcallDiagram.png|500px]]
=== Why GotCloud?===
Many of the same reasons as using GotCloud align
* Easy to learn & run
** All-in-one package for '''snp calling pipeline'''
** You don’t have to know the details of individual component
* Robust parallelization
** Automatic partitions '''by regions'''
** Reliable and fault-tolerant parallelization via GNU make
*** Restart from where it stopped upon unexpected crash
* Cloud & Cluster-friendly
** Supports multiple clusters such as MOSIX, Slurm, & SGE
** Amazon instances allow running large-scale jobs without having your own cluster
* '''Easy to add new samples to your study'''
** Just add them to your index
** GotCloud will reuse the genotype likelihoods for samples already completed
{{SeqShopLogin}}
== Setup your run environment ==
This will setup some environment variables to point you to the Tutorial files as well as to an output directory.
source /home/mktrost/seqshop/setup.txt
Alternatively, if you would like to change the output directory, copy the file, make the modifications and source your file:
cp /home/mktrost/seqshop/setup.txt ~/setup.txt
nedit ~/setup.txt
source ~/setup.txt
(You can use your favorite editor instead of nedit. I typically use emacs, but nedit is more like Windows.)
== Examining GotCloud SnpCall Input files ==
=== Sequnce Alignment Files: BAM Files ===
=== Reference Files ===
=== GotCloud BAM Index File ===
=== GotCloud Configuration File ===
We will use the same configuration file as we used yesterday in GotCloud Align.
== Run GotCloud SnpCall ==
Now that we have all of our input files, we need just a simple command to run:
${GC}/gotcloud/gotcloud snpcall --conf ${GC}/inputs/gotcloud.conf --numjobs 4 --region 22:36000000-37000000
* --numjobs tells GotCloud how many jobs to run in parallel
** Depends on your system
* --region 22:36000000-37000000
** The sample files are just a small region of chromosome 22, so to save time, we tell Gotcloud to ignore the other regions
This should take about 5 minutes to run.
It should end with a line like: <code>TBD</code>
If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off.
== Examining GotCloud SnpCall Output ==
=== Filtering Summary Statistics ===
cat ${OUTPUT}/vcfs/chr22/chr22.filtered.sites.vcf.summary
<div class="mw-collapsible mw-collapsed" style="width:250px">
View Annotated Screenshot
<div class="mw-collapsible-content">
[[File:filterSum.png]]
</div>
</div>
== GotCloud Genotype Refinement ==
seqshop/gotcloud/gotcloud beagle --conf seqshop/inputs/gotcloud.conf --numjobs 2 --region 22:36000000-37000000
seqshop/gotcloud/gotcloud beagle --conf seqshop/inputs/gotcloud.conf --numjobs 2 --region 22:36000000-37000000
