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Revision as of 18:35, 19 August 2015
, 18:35, 19 August 2015→Filtered VCF: since the uncompressed vcf isn't created, use zless on the compressed
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=== Prerequisite Tutorials ===
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|Alignment Tutorial]]
Now that we have all of our input files, we need just a simple command to run:
Now that we have all of our input files, we need just a simple command to run:
* When running at home if you don't have 6 CPUs, reduce the --numjobs setting (it will take longer to run).
* When running at home if you don't have 8 CPUs, reduce the --numjobs setting (it will take longer to run).
${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 6 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>${GC}/gotcloud</code> runs GotCloud
* <code>snpcall</code> tells GotCloud you want to run the snpcall pipeline.
* <code>snpcall</code> tells GotCloud you want to run the snpcall pipeline.
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This should take about 5-8 minutes to run.
This should take about 3-6 minutes to run.
* It should end with a line like: <code>Commands finished in 402 secs with no errors reported</code>
* It should end with a line like: <code>Commands finished in 402 secs with no errors reported</code>
Let's look at the filtered sites file.
Let's look at the filtered sites file.
zless -S ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.gz
* Scroll down until you find some variants.
* Scroll down until you find some variants.
=== Running GotCloud Genotype Refinement ===
=== Running GotCloud Genotype Refinement ===
Since everything is setup, just run the following command (very similar to snpcall).
Since everything is setup, just run the following command (very similar to snpcall).
${GC}/gotcloud ldrefine --conf ${SS}/gotcloud.conf --numjobs 6 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
${GC}/gotcloud ldrefine --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT}
* Beagle will take about 1-3 minutes to complete
* Beagle will take about 1-3 minutes to complete
<li><code>1|1</code>; Homozygous Alt (C)</li>
<li><code>1|1</code>; Homozygous Alt (C)</li>
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Note the '|' instead of '/'. The '|' indicates it is now phased.
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