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Jump to navigationJump to search→STEP 3 : Run GotCloud Variant Calling Pipeline
Run the variant calling pipeline:
Run the variant calling pipeline:
~/gotcloud/gotcloud snpcall --conf ~/gotcloudExample/[[GBR60vc.conf]] --outdir ~/gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix ~/gotcloudExample
cd ~
gotcloud/gotcloud snpcall --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix gotcloudExample
Upon successful completion of the variant calling pipeline (about 3-4 minutes), you will see the following message:
Upon successful completion of the variant calling pipeline (about 3-4 minutes), you will see the following message:
On SNP Call success, the VCF files of interest are:
On SNP Call success, the VCF files of interest are:
ls ~/gotcloudTutorialOut/vcfs/chr20/chr20.filtered*
ls gotcloudTutorialOut/vcfs/chr20/chr20.filtered*
This gives you the following files:
This gives you the following files:
Note: the tutorial does not produce a target directory, but if you run with targeted data, you may see that.
Note: the tutorial does not produce a target directory, but if you run with targeted data, you may see that.
== STEP 4 : Run GotCloud Genotype Refinement Pipeline ==
== STEP 4 : Run GotCloud Genotype Refinement Pipeline ==
