diff --git a/scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala b/scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala index 913a58f0f..44269e70d 100755 --- a/scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala +++ b/scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala @@ -29,7 +29,7 @@ class Phase1Cleaning extends QScript { private val tmpDir: File = new File("/broad/shptmp/rpoplin/tmp/") private val reference: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta") - private val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.vcf") + private val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf") private val dindelPilotCalls: String = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg.pilot_release.merged.indels.sites.hg19.vcf" private val dindelAFRCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110111_august_dindel_indel_calls/AFR.dindel_august_release.20110110.sites.vcf.gz" private val dindelASNCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110111_august_dindel_indel_calls/ASN.dindel_august_release.20110110.sites.vcf.gz" @@ -96,4 +96,4 @@ class Phase1Cleaning extends QScript { } } -} \ No newline at end of file +}