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Run the variant calling pipeline:
Run the variant calling pipeline:
~/gotcloud/gotcloud snpcall --conf [[GBR60vc.conf]] --outdir ~/gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000
~/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:
This gives you the following files:
This gives you the following files:
* '''chr20.filtered.vcf.gz ''' - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL including per sample genotypes
* '''chr20.filtered.vcf.gz ''' - vcf for whole chromosome after it has been run through hardfilters and SVM filters and marked with PASS/FAIL including per sample genotypes
* chr20.filtered.sites.vcf - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL without the per sample genotypes
* chr20.filtered.sites.vcf - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL without the per sample genotypes
* chr20.filtered.sites.vcf.log - log file
* chr20.filtered.sites.vcf.norm.log - log file
* chr20.filtered.sites.vcf.summary - summary of filters applied
* chr20.filtered.sites.vcf.summary - summary of filters applied
* chr20.filtered.vcf.gz.OK - indicator that the filtering completed successfully
* chr20.filtered.vcf.gz.OK - indicator that the filtering completed successfully
** chr20.merged.vcf - including per sample genotypes
** chr20.merged.vcf - including per sample genotypes
** chr20.merged.vcf.OK - indicator that the step completed successfully
** chr20.merged.vcf.OK - indicator that the step completed successfully
* the hardfiltered (pre-svm filtered) variant calls:
** chr20.filtered.vcf.gz - vcf for whole chromosome after it has been run through hard filters
** chr20.hardfiltered.sites.vcf - vcf for whole chromosome after it has been run through filters and marked with PASS/FAIL without the per sample genotypes
** chr20.hardfiltered.sites.vcf.log - log file
** chr20.hardfiltered.sites.vcf.summary - summary of filters applied
** chr20.hardfiltered.vcf.gz.OK - indicator that the filtering completed successfully
** chr20.hardfiltered.vcf.gz.tbi - index file for the vcf file
* 40000001.45000000 subdirectory contains the data for just that region.
* 40000001.45000000 subdirectory contains the data for just that region.
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 5 : Run GotCloud Genotype Refinement Pipeline ==
== STEP 5 : Run GotCloud Genotype Refinement Pipeline ==
Run the LD-aware genotype refinement pipeline:
Run the LD-aware genotype refinement pipeline:
~/gotcloud/gotcloud ldrefine --conf [[GBR60vc.conf]] --outdir ~/gotcloudTutorialOut --numjobs 2
~/gotcloud/gotcloud ldrefine --conf ~/gotcloudExample/[[GBR60vc.conf]] --outdir ~/gotcloudTutorialOut --numjobs 2 --baseprefix ~/gotcloudExample
Upon successful completion of this pipeline, you will see the following message:
Upon successful completion of this pipeline, you will see the following message:
