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, 18:35, 19 August 2015
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| </div> | | </div> |
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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 | + | zless -S ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.gz |
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| * 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} | + | ${GC}/gotcloud ldrefine --conf ${SS}/gotcloud.conf --numjobs 8 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT} |
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| * 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> |
| </ul> | | </ul> |
| + | Note the '|' instead of '/'. The '|' indicates it is now phased. |
| </div> | | </div> |
| </div> | | </div> |