Changes

Instead, let's look what the output would have looked like.

Instead, let's look what the output would have looked like.

  ls $IN/metadata

  ls ${SS}/svtoolkit/metadata

  cpt  depth  depth.dat  gcprofile  gcprofiles.zip  genome_sizes.txt  isd  isd.dist.bin  spans  spans.dat

  cpt  depth  depth.dat  gcprofile  gcprofiles.zip  genome_sizes.txt  isd  isd.dist.bin  spans  spans.dat

See [[http://gatkforums.broadinstitute.org/discussion/1514/svpreprocess-queue-script]] for the details of the Preprocess step.

See [[http://gatkforums.broadinstitute.org/discussion/1514/svpreprocess-queue-script]] for the details of the Preprocess step.

NOTE: You don't always have to create the metadata on your own. You can in principle use the public metadata generated for 1000G samples, under the assumption that the metadata share similar characteristics to your samples. But if you have enough computing resources, the best practice is to create metadata specifically for your sequence daat.

NOTE: You don't always have to create the metadata on your own. You can in principle use the public metadata generated for 1000G samples, under the assumption that the metadata share similar characteristics to your samples. But if you have enough computing resources, the best practice is to create metadata specifically for your sequence data.

== Running GotCloud/GenomeSTRiP Discovery Pipeline ==

== Running GotCloud/GenomeSTRiP Discovery Pipeline ==