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Commit 4a7474a4 authored by Ruben Vorderman's avatar Ruben Vorderman
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GenotypeGVCFs only works on a single file

parent 20c4c217
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......@@ -725,8 +725,8 @@ task GatherBqsrReports {
task GenotypeGVCFs {
input {
Array[File]+ gvcfFiles
Array[File]+ gvcfFilesIndex
File gvcfFile
File gvcfFileIndex
Array[File]+ intervals
String outputPath
File referenceFasta
......@@ -751,7 +751,7 @@ task GenotypeGVCFs {
-G StandardAnnotation \
--only-output-calls-starting-in-intervals \
-new-qual \
-V ~{sep=' -V ' gvcfFiles} \
-V ~{gvcfFile} \
-L ~{sep=' -L ' intervals}
}
......
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