Changes

Run the alignment pipeline (the example aligns 2 samples) :  

Run the alignment pipeline (the example aligns 2 samples) :  

  ~/gotcloud/gotcloud align --conf ~/gotcloudExample/[[#Alignment Configuration File|GBR2align.conf]] --outdir [[#Alignment Output Directory|~/gotcloudTutorialOut]]  

  ~/gotcloud/gotcloud align --conf ~/gotcloudExample/[[#Alignment Configuration File|GBR2align.conf]] --outdir [[#Alignment Output Directory|~/gotcloudTutorialOut]] --baseprefix ~/gotcloudExample

Upon successful completion of the alignment pipeline (about 1-2 minutes), you will see the following message:  

Upon successful completion of the alignment pipeline (about 1-2 minutes), you will see the following message:  

For information on the VerifyBamID output, see: [[Understanding VerifyBamID output]]  

For information on the VerifyBamID output, see: [[Understanding VerifyBamID output]]  

For information on the QPLOT output, see: [[Understanding QPLOT output]]  

For information on the QPLOT output, see: [[Understanding QPLOT output]]

== STEP 3 : Run GotCloud Variant Calling Pipeline ==  

== STEP 3 : Run GotCloud Variant Calling Pipeline ==