From 9b432d08010867bda11c1d242d3e45d0138a44b5 Mon Sep 17 00:00:00 2001 From: depristo Date: Tue, 10 Aug 2010 12:01:18 +0000 Subject: [PATCH] 1kg script now works git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3998 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/depristo/1kg_table1.scala | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/scala/qscript/depristo/1kg_table1.scala b/scala/qscript/depristo/1kg_table1.scala index 9434137a1..e307390ad 100755 --- a/scala/qscript/depristo/1kg_table1.scala +++ b/scala/qscript/depristo/1kg_table1.scala @@ -10,7 +10,10 @@ class Onekg_table1 extends QScript { @Argument(doc="gatkJarFile") var gatkJarFile: File = _ -trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile } // -L 1 + @Argument(shortName = "R", doc="gatkJarFile") + var referenceFile: File = _ + +trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; reference_sequence = referenceFile } // -L 1 class Target(project: String, snpVCF: String, indelVCF: String, calledGenome: Double, targetGenome: Double, pop: String, pilot : String, bam: String = null) { def reportFile: String = List(pop, pilot, "report").mkString(".") @@ -71,7 +74,7 @@ def script = stage match { for ( (pop: String,called) <- p1Targets ) { val auto = "/humgen/gsa-hpprojects/1kg/releases/pilot_paper_calls/low_coverage/snps/"+ pop +".low_coverage.2010_07.genotypes.vcf.gz" // todo -- remove fixed when Laura gives us the official calls - val x = "/humgen/gsa-hpprojects/1kg/releases/pilot_paper_calls/low_coverage/snps/"+ pop +".low_coverage.2010_07.xchr.fixed.genotypes.vcf.gz" + val x = "/humgen/gsa-hpprojects/1kg/releases/pilot_paper_calls/low_coverage/snps/"+ pop +".low_coverage.2010_07.xchr.fixed.genotypes.vcf" val combineSNPs = new Combine(List(auto, x), pop + ".pilot1.vcf") add(combineSNPs) } @@ -93,14 +96,14 @@ def script = stage match { val snps = "1kg.snps.merged.vcf" val indels = "1kg.indels.merged.vcf" - add(new Combine(pilots.map(_ + ".snps.merged.vcf"), snps)) + //add(new Combine(pilots.map(_ + ".snps.merged.vcf"), snps)) add(new Combine(pilots.map(_ + ".indels.merged.vcf"), indels)) // VariantEval of the SNPs - for (target <- targets) { - add(new VariantEval(target.getSNPVCF, target.getSNPEval)) - add(new StatPop(target)) - } + //for (target <- targets) { + // add(new VariantEval(target.getSNPVCF, target.getSNPEval)) + // add(new StatPop(target)) + //} case "DOC" => for (target <- targets) {