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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:
Commands finished in xxx secs with no errors reported
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:
The next step is to perform genotype refinement using linkage disequilibrium information using [http://faculty.washington.edu/browning/beagle/beagle.html Beagle] & [[ThunderVCF]].
The next step is to perform genotype refinement using linkage disequilibrium information using [http://faculty.washington.edu/browning/beagle/beagle.html Beagle] & [[ThunderVCF]].
Run the LD-aware genotype refinement pipeline:
$GCHOME/gotcloud ldrefine --conf [[GBR60vc.conf]] --outdir $GCOUT --numjobs 2
$GCHOME/gotcloud ldrefine --conf [[GBR60vc.conf]] --outdir $GCOUT --numjobs 2
Upon successful completion of this pipeline, you will see the following message:
Commands finished in xxx secs with no errors reported
== STEP 5 : Run GotCloud Association Analysis Pipeline ==
== STEP 5 : Run GotCloud Association Analysis Pipeline ==
/net/fantasia/home/hmkang/bin/epacts/bin/epacts single --vcf gotcloud/test_data/UMAKE_OUT/vcfs/chr20/chr20.filtered.vcf.gz --ped gotcloud/test_data/gotcloudExample/test.GBR60.ped --out EPACTS_TEST --test q.linear --run -1 --top 1 --chr 20
/net/fantasia/home/hmkang/bin/epacts/bin/epacts single --vcf $GCOUT/vcfs/chr20/chr20.filtered.vcf.gz --ped $GCDATA/test.GBR60.ped --out EPACTS_TEST --test q.linear --run -1 --top 1 --chr 20
