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 --snpcall --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 final VCF produced by the variant calling pipeline containing only the variants that passed all filters is:

The final VCF produced by the variant calling pipeline containing only the variants that passed all filters is:

  ls vcResults/split/chr20/chr20.filtered.PASS.vcf.gz

  ls $GCOUT/split/chr20/chr20.filtered.PASS.vcf.gz

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 vcResults/vcf/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 ==

Instructions for running Beagle/Thunder.

The next step is to perform genotype refinement using linkage disequilibrium information using [http://faculty.washington.edu/browning/beagle/beagle.html Beagle] & [[ThunderVCF]].

 

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