diff --git a/scala/qscript/oneoffs/carneiro/mendelianViolation.scala b/scala/qscript/oneoffs/carneiro/mendelianViolation.scala index e285bfa60..3024046cf 100755 --- a/scala/qscript/oneoffs/carneiro/mendelianViolation.scala +++ b/scala/qscript/oneoffs/carneiro/mendelianViolation.scala @@ -1,6 +1,6 @@ import java.io.File import org.broadinstitute.sting.commandline.Argument -import org.broadinstitute.sting.queue.extensions.gatk.{SelectVariants, RodBind} +import org.broadinstitute.sting.queue.extensions.gatk.{SelectVariants, RodBind, VariantsToTable} import org.broadinstitute.sting.queue.QScript /* @@ -13,11 +13,11 @@ import org.broadinstitute.sting.queue.QScript class mendelianViolation extends QScript { - @Argument(shortName="trio", doc="input trio VCF file", required=false) - var trio: File = new File("/home/radon00/carneiro/prj/trio/analysis/calls/CEUTrio.WEx.recalibrated.vcf") + @Argument(shortName="trio", doc="input trio VCF file", required=true) + var trio: File = _ - @Argument(shortName="daughter", doc="daughter input VCF file", required=false) - var daughter: File = "/humgen/gsa-hpprojects/dev/rpoplin/perfectCalls/NA12878/chart/sting/NA12878.HiSeq19.recalibrated.hapmapCut.vcf" + @Argument(shortName="daughter", doc="daughter input VCF file", required=true) + var daughter: File = _ @Argument(shortName="family", doc="family string", required=false) var family: String = "NA12891+NA12892=NA12878"