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

Updating dbsnp to v135

This commit is contained in:
Eric Banks 2012-03-12 13:17:58 -04:00
parent 7e9a535c4d
commit 359090c4b7
1 changed files with 4 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
View File

@ -81,7 +81,7 @@ class GATKResourcesBundle extends QScript {
def initializeTestDataFiles() = { def initializeTestDataFiles() = {
// //
// Standard evaluation files for indels // Standard evaluation files for indel
// //
b37 = new Reference("b37", new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta")) b37 = new Reference("b37", new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta"))
hg18 = new Reference("hg18", new File("/Users/depristo/Desktop/broadLocal/localData/Homo_sapiens_assembly18.fasta")) hg18 = new Reference("hg18", new File("/Users/depristo/Desktop/broadLocal/localData/Homo_sapiens_assembly18.fasta"))
@ -122,8 +122,8 @@ class GATKResourcesBundle extends QScript {
// //
// standard VCF files. Will be lifted to each reference // standard VCF files. Will be lifted to each reference
// //
addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_132_b37.leftAligned.vcf", addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_135_b37.leftAligned.vcf",
"dbsnp_132", 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_genotypes_1525_samples.b37.vcf",
"1000G_omni2.5", b37, true, true)) "1000G_omni2.5", b37, true, true))
@ -132,7 +132,7 @@ class GATKResourcesBundle extends QScript {
"hapmap_3.3", b37, true, true)) "hapmap_3.3", b37, true, true))
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_phase2.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, true))