Commit ff6840c5 authored by Wai Yi Leung's avatar Wai Yi Leung

Fix clever vcf header and add sorting step

parent ab7e15d4
......@@ -81,6 +81,7 @@ object CleverFixVCF extends ToolCommand {
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=BPWINDOW,Number=2,Type=Integer,Description="Window of breakpoints">
##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around the inserted material between breakends">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency">
......
......@@ -15,7 +15,8 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import nl.lumc.sasc.biopet.extensions.clever.{ CleverCaller, CleverFixVCF }
import nl.lumc.sasc.biopet.extensions.clever.{CleverCaller, CleverFixVCF}
import nl.lumc.sasc.biopet.extensions.picard.SortVcf
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler Clever */
......@@ -31,11 +32,17 @@ class Clever(val root: Configurable) extends SvCaller {
val cleverVCF = new CleverFixVCF(this)
cleverVCF.input = clever.outputvcf
cleverVCF.output = new File(cleverDir, s"${sample}.clever.vcf")
cleverVCF.output = new File(cleverDir, s".${sample}.clever.vcf")
cleverVCF.sampleName = sample
cleverVCF.isIntermediate = true
add(cleverVCF)
addVCF(sample, cleverVCF.output)
val sortvcf = new SortVcf(this)
sortvcf.input = cleverVCF.output
sortvcf.output = new File(cleverDir, s"${sample}.clever.vcf")
add(sortvcf)
addVCF(sample, sortvcf.output)
}
}
}
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