From 418fbdfbabcd61c8c3a5d5af4ef07cc29c0f7e30 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sat, 7 Dec 2013 21:03:27 -0500 Subject: [PATCH] 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. --- .../queue/qscripts/GATKResourcesBundle.scala | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala index 307ce171f..d0c917a9e 100644 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala @@ -168,11 +168,18 @@ class GATKResourcesBundle extends QScript { "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", - "CEUTrio.HiSeq.WGS.b37.bestPractices.phased",b37,true,false)) + 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",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 @@ -290,9 +297,8 @@ class GATKResourcesBundle extends QScript { } } - createCurrentLink(BUNDLE_DIR) - } else { + createCurrentLink(BUNDLE_DIR) createBundleDirectories(DOWNLOAD_DIR) createDownloadsFromBundle(BUNDLE_DIR, DOWNLOAD_DIR) }