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
" + + "
" + "

Usage example:

" + "
" +
             "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")