From 5ea7cd6dcc612e8e284a4faaccc0222302565e0f Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 31 Aug 2012 14:01:54 -0400 Subject: [PATCH] Updating resource bundle: no reason to include both genotype and sites files for Omni and HM3, sites are enough. Also, don't include duplicate entry for the Mills indels. --- .../sting/queue/qscripts/GATKResourcesBundle.scala | 10 +++++----- 1 file changed, 5 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 3dc953361..08496e284 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala @@ -125,17 +125,17 @@ class GATKResourcesBundle extends QScript { addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_135_b37.leftAligned.vcf", "dbsnp_135", b37, true, false)) - addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni25_genotypes_1525_samples.b37.vcf", - "1000G_omni2.5", b37, true, true)) + addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni25_sites_2141_samples.b37.vcf", + "1000G_omni2.5", b37, true, false)) - 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/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf", + "hapmap_3.3", b37, true, false)) addResource(new Resource("/humgen/1kg/DCC/ftp/technical/working/20120312_phase1_v2_indel_cleaned_sites_list/ALL.wgs.phase1_release_v2.20101123.official_indel_calls.20120312.sites.vcf", "1000G_phase1.indels", b37, true, false)) addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf", - "Mills_and_1000G_gold_standard.indels", b37, true, true)) + "Mills_and_1000G_gold_standard.indels", b37, true, false)) // // example call set for wiki tutorial