zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

16
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
View File

@ -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)
}