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1kg script now works 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3998 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-08-10 12:01:18 +00:00
parent d514c424fd
commit 9b432d0801
1 changed files with 10 additions and 7 deletions
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17
scala/qscript/depristo/1kg_table1.scala
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@ -10,7 +10,10 @@ class Onekg_table1 extends QScript {
@Argument(doc="gatkJarFile") @Argument(doc="gatkJarFile")
var gatkJarFile: File = _ 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) { 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(".") def reportFile: String = List(pop, pilot, "report").mkString(".")
@ -71,7 +74,7 @@ def script = stage match {
for ( (pop: String,called) <- p1Targets ) { 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" 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 // 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") val combineSNPs = new Combine(List(auto, x), pop + ".pilot1.vcf")
add(combineSNPs) add(combineSNPs)
} }
@ -93,14 +96,14 @@ def script = stage match {
val snps = "1kg.snps.merged.vcf" val snps = "1kg.snps.merged.vcf"
val indels = "1kg.indels.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)) add(new Combine(pilots.map(_ + ".indels.merged.vcf"), indels))
// VariantEval of the SNPs // VariantEval of the SNPs
for (target <- targets) { //for (target <- targets) {
add(new VariantEval(target.getSNPVCF, target.getSNPEval)) // add(new VariantEval(target.getSNPVCF, target.getSNPEval))
add(new StatPop(target)) // add(new StatPop(target))
} //}
case "DOC" => case "DOC" =>
for (target <- targets) { for (target <- targets) {