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== Goals of This Session == * What we want to learn ** How to generate filtered variant calls for SNPs from BAMs ** Basic variant call file format (VCF) ** How to examine the variants at particular genomic positions ** How to evaluate the quality of SNP calls == 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

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