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Jump to navigationJump to search→STEP 3 : Run GotCloud Variance Calling Pipeline
Run the variant calling pipeline:
Run the variant calling pipeline:
$GCHOME/gotcloud snpcall --conf [[GBR60vc.conf]] --outdir $GCOUT --numjobs 2
$GCHOME/gotcloud snpcall --conf [[GBR60vc.conf]] --outdir $GCOUT --numjobs 2 --region 20:42900000-43200000
Upon successful completion of the variant calling pipeline, you will see the following message:
Upon successful completion of the variant calling pipeline (about 3-4 minutes), you will see the following message:
Commands finished in nnn secs with no errors reported
Commands finished in nnn secs with no errors reported
