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, 15:21, 2 August 2013
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| Run the LD-aware genotype refinement pipeline: | | Run the LD-aware genotype refinement pipeline: |
− | ~/gotcloud/gotcloud ldrefine --conf ~/gotcloudExample/[[GBR60vc.conf]] --outdir ~/gotcloudTutorialOut --numjobs 2 --baseprefix ~/gotcloudExample | + | cd ~ |
| + | gotcloud/gotcloud ldrefine --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --baseprefix gotcloudExample |
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| Upon successful completion of this pipeline (about 10 minutes), you will see the following message: | | Upon successful completion of this pipeline (about 10 minutes), you will see the following message: |
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| The output from the beagle step of the genotype refinement pipeline is found in: | | The output from the beagle step of the genotype refinement pipeline is found in: |
− | ls ~/gotcloudTutorialOut/beagle/chr20/chr20.filtered.PASS.beagled.vcf.gz ~/gotcloudTutorialOut/beagle/chr20/chr20.filtered.PASS.beagled.vcf.gz.tbi | + | ls gotcloudTutorialOut/beagle/chr20/chr20.filtered.PASS.beagled.vcf.gz gotcloudTutorialOut/beagle/chr20/chr20.filtered.PASS.beagled.vcf.gz.tbi |
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| The output from the thunderVcf (final step) of the genotype refinement pipeline is found in: | | The output from the thunderVcf (final step) of the genotype refinement pipeline is found in: |
− | ls ~/gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz ~/gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi | + | ls gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz gotcloudTutorialOut/thunder/chr20/GBR/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi |
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| == STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) == | | == STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) == |