From d0e7ab33e767e7446b50db5cf0aaead080bfa3fe Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Fri, 13 Jan 2017 13:52:25 +0100
Subject: [PATCH 1/2] add IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS); to
 MergeVcfs

---
 src/main/java/picard/vcf/MergeVcfs.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/java/picard/vcf/MergeVcfs.java b/src/main/java/picard/vcf/MergeVcfs.java
index ee0ae76bc..21b2cdf6f 100644
--- a/src/main/java/picard/vcf/MergeVcfs.java
+++ b/src/main/java/picard/vcf/MergeVcfs.java
@@ -94,6 +94,8 @@ public MergeVcfs() {
     protected int doWork() {
         final ProgressLogger progress = new ProgressLogger(log, 10000);
         final List<String> sampleList = new ArrayList<String>();
+        INPUT = IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS);
+        for (final File f: INPUT) IOUtil.assertFileIsReadable(f);
         final Collection<CloseableIterator<VariantContext>> iteratorCollection = new ArrayList<CloseableIterator<VariantContext>>(INPUT.size());
         final Collection<VCFHeader> headers = new HashSet<VCFHeader>(INPUT.size());
 

From 629758727de208a06055a2c1fd57c05943bd79a1 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Fri, 13 Jan 2017 16:57:04 +0100
Subject: [PATCH 2/2] answer to
 https://github.com/broadinstitute/picard/pull/729#pullrequestreview-16581170

---
 src/main/java/picard/vcf/MergeVcfs.java | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/main/java/picard/vcf/MergeVcfs.java b/src/main/java/picard/vcf/MergeVcfs.java
index 21b2cdf6f..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<File> INPUT;
 
     @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The merged VCF or BCF file. File format is determined by file extension.")
@@ -95,7 +95,6 @@ protected int doWork() {
         final ProgressLogger progress = new ProgressLogger(log, 10000);
         final List<String> sampleList = new ArrayList<String>();
         INPUT = IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS);
-        for (final File f: INPUT) IOUtil.assertFileIsReadable(f);
         final Collection<CloseableIterator<VariantContext>> iteratorCollection = new ArrayList<CloseableIterator<VariantContext>>(INPUT.size());
         final Collection<VCFHeader> headers = new HashSet<VCFHeader>(INPUT.size());