diff --git a/src/main/java/picard/vcf/MergeVcfs.java b/src/main/java/picard/vcf/MergeVcfs.java index ee0ae76bc..6f9d0c9a0 100644 --- a/src/main/java/picard/vcf/MergeVcfs.java +++ b/src/main/java/picard/vcf/MergeVcfs.java @@ -71,7 +71,7 @@ ) public class MergeVcfs extends CommandLineProgram { - @Option(shortName= StandardOptionDefinitions.INPUT_SHORT_NAME, doc="VCF or BCF input files File format is determined by file extension.", minElements=1) + @Option(shortName= StandardOptionDefinitions.INPUT_SHORT_NAME, doc="VCF or BCF input files (File format is determined by file extension), or a file having a '.list' suffix containing the path to the files.", minElements=1) public List INPUT; @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The merged VCF or BCF file. File format is determined by file extension.") @@ -94,6 +94,7 @@ public MergeVcfs() { protected int doWork() { final ProgressLogger progress = new ProgressLogger(log, 10000); final List sampleList = new ArrayList(); + INPUT = IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS); final Collection> iteratorCollection = new ArrayList>(INPUT.size()); final Collection headers = new HashSet(INPUT.size());