diff --git a/src/main/java/picard/util/BedToIntervalList.java b/src/main/java/picard/util/BedToIntervalList.java
index 886a40e5d..5170c100a 100644
--- a/src/main/java/picard/util/BedToIntervalList.java
+++ b/src/main/java/picard/util/BedToIntervalList.java
@@ -64,9 +64,16 @@
" -Strand - Indicates +/- strand for the interval (either + or -)
" +
" -Interval name - (Each interval should have a unique name) " +
"" +
- "
" +
- "This tool requires sequence dictionary file (with \".dict\" extension), which can be created from a reference sequence " +
- "using Picard's CreateSequenceDictionary tool."+
+ "
" +
+ "This tool requires a sequence dictionary, provided with the SEQUENCE_DICTIONARY or SD argument. " +
+ "The value given to this argument can be any of the following:" +
+ "
" + + " - A file with .dict extension generated using Picard's CreateSequenceDictionaryTool" + + " - A reference.fa or reference.fasta file with a reference.dict in the same directory" + + " - Another IntervalList with @SQ lines in the header from which to generate a dictionary" + + " - A VCF that contains #contig lines from which to generate a sequence dictionary" + + " - A SAM or BAM file with @SQ lines in the header from which to generate a dictionary" + + "" + "
" +
"java -jar picard.jar BedToIntervalList \\
" +
@@ -80,7 +87,8 @@
@Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input BED file")
public File INPUT;
- @Option(shortName = StandardOptionDefinitions.SEQUENCE_DICTIONARY_SHORT_NAME, doc = "The sequence dictionary")
+ @Option(shortName = StandardOptionDefinitions.SEQUENCE_DICTIONARY_SHORT_NAME,
+ doc = "The sequence dictionary, or BAM/VCF/IntervalList from which a dictionary can be extracted.")
public File SEQUENCE_DICTIONARY;
@Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The output Picard Interval List")