From 85626e7a5dbae8a263b8e2ff2e64bd25656d6e9c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 19 Sep 2011 12:24:05 -0400 Subject: [PATCH] We no longer want people to use the August 2010 Dindel calls for indel realignment but instead Guillermo's new whole genome bi-allelic indel calls; updating the bundle accordingly. Also, there was some confusion by the 1000G data processing folks as to exactly what these indel files are, so I've renamed them so that it's clear. Wiki updated too. --- .../sting/queue/qscripts/GATKResourcesBundle.scala | 6 +++--- 1 file changed, 3 insertions(+), 3 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 59c00b8cd..e8b8258c1 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala @@ -131,11 +131,11 @@ class GATKResourcesBundle extends QScript { addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf", "hapmap_3.3", b37, true, true)) - addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf", - "1000G_indels_for_realignment", b37, true, false)) + addResource(new Resource("/humgen/1kg/processing/official_release/phase1/ALL.wgs.VQSR_consensus_biallelic.20101123.indels.sites.vcf", + "1000G_biallelic.indels", b37, true, false)) addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Mills_Devine_Indels_2011/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.vcf", - "indels_mills_devine", b37, true, true)) + "Mills_Devine_2hit.indels", b37, true, true)) // // example call set for wiki tutorial