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Jump to navigationJump to search→STEP 4 : Run GotCloud Genotype Refinement Pipeline
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
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:
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
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
== STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) ==
== STEP 5 : Run GotCloud Association Analysis Pipeline (EPACTS) ==
