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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.

This commit is contained in:
Eric Banks 2012-08-31 14:01:54 -04:00
parent f066a02f3e
commit 5ea7cd6dcc
1 changed files with 5 additions and 5 deletions
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10
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
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@ -125,17 +125,17 @@ class GATKResourcesBundle extends QScript {
addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_135_b37.leftAligned.vcf", addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_135_b37.leftAligned.vcf",
"dbsnp_135", b37, true, false)) "dbsnp_135", b37, true, false))
addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni25_genotypes_1525_samples.b37.vcf", addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni25_sites_2141_samples.b37.vcf",
"1000G_omni2.5", b37, true, true)) "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", addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf",
"hapmap_3.3", b37, true, true)) "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", 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)) "1000G_phase1.indels", b37, true, false))
addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf", 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 // example call set for wiki tutorial