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Added HC trio calls and NA12878 KB snapshot to resource bundle. 

Also, don't touch the current link until the resources are finished being produced.
This commit is contained in:
Eric Banks 2013-12-07 21:03:27 -05:00
parent 932cd3ada7
commit 418fbdfbab
1 changed files with 11 additions and 5 deletions
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16
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
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@ -168,11 +168,18 @@ class GATKResourcesBundle extends QScript {
"Mills_and_1000G_gold_standard.indels", b37, true, false)) "Mills_and_1000G_gold_standard.indels", b37, true, false))
// //
// CEU trio (NA12878,NA12891,NA12892) best practices results (including PBT) // CEU trio (NA12878,NA12891,NA12892) best practices results
// //
addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/callsets/CEUtrio_BestPractices/CEUTrio.HiSeq.WGS.b37.snps_and_indels.recalibrated.filtered.phased.CURRENT.vcf", addResource(new Resource("/humgen/1kg/processing/production_wgs_final/trio/CEU/CEU.wgs.HaplotypeCaller.20131118.snps_indels.high_coverage_pcr_free.genotypes.vcf",
"CEUTrio.HiSeq.WGS.b37.bestPractices.phased",b37,true,false)) "CEUTrio.HiSeq.WGS.b37.bestPractices",b37,true,false))
//
// NA12878 knowledgebase snapshot
//
addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/knowledgeBase/snapshots/NA12878.wgs.broad_truth_set.20131119.snps_and_indels.genotypes.vcf",
"NA12878.knowledgebase.snapshot.20131119",b37,true,false))
// //
// example call set for documentation guide tutorial // example call set for documentation guide tutorial
@ -290,9 +297,8 @@ class GATKResourcesBundle extends QScript {
} }
} }
createCurrentLink(BUNDLE_DIR)
} else { } else {
createCurrentLink(BUNDLE_DIR)
createBundleDirectories(DOWNLOAD_DIR) createBundleDirectories(DOWNLOAD_DIR)
createDownloadsFromBundle(BUNDLE_DIR, DOWNLOAD_DIR) createDownloadsFromBundle(BUNDLE_DIR, DOWNLOAD_DIR)
} }