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→‎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]]
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Let's look at the filtered sites file.
 
Let's look at the filtered sites file.
  less -S ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf
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  zless -S ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.gz
    
* Scroll down until you find some variants.
 
* Scroll down until you find some variants.
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=== 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}
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  ${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
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<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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