Changes

Run the variant calling pipeline:

Run the variant calling pipeline:

  $GCHOME/gotcloud snpcall --conf [[GBR60vc.conf]] --outdir $GCOUT --snpcall --numjobs 2

  $GCHOME/gotcloud snpcall --conf [[GBR60vc.conf]] --outdir $GCOUT --numjobs 2

Upon successful completion of the variant calling pipeline, you will see the following message:  

Upon successful completion of the variant calling pipeline, you will see the following message:  

The VCF including the filtered sites with the filters marked in the Filter field (or "PASS" if the site was not filtered) is:

The VCF including the filtered sites with the filters marked in the Filter field (or "PASS" if the site was not filtered) is:

  ls $GCOUT/vcfs/chr20/chr20.filtered.vcf.gz

  ls $GCOUT/vcfs/chr20/chr20.filtered.vcf.gz

== STEP 4 : Run GotCloud Genotype Refinement Pipeline ==

== STEP 4 : Run GotCloud Genotype Refinement Pipeline ==