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Always best to use the left-aligned version of the dbsnp vcf 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5091 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-26 20:21:50 +00:00
parent 43812a28fc
commit 68729045ca
1 changed files with 2 additions and 2 deletions
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4
scala/qscript/oneoffs/rpoplin/Phase1Cleaning.scala
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@ -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 {
}
}
}
}