diff --git a/src/main/java/picard/sam/DownsampleSam.java b/src/main/java/picard/sam/DownsampleSam.java index 06b69d5c5..41822d511 100644 --- a/src/main/java/picard/sam/DownsampleSam.java +++ b/src/main/java/picard/sam/DownsampleSam.java @@ -73,10 +73,11 @@ "
" +
             "java -jar picard.jar DownsampleSam \\
" + " I=input.bam \\
" + + " METRICS_FILE=downsample_metrics.txt \\
" + " O=downsampled.bam" + "
" + "
"; - @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input SAM or BAM file to downsample.") + @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input SAM or BAM file to downsample. Starting v2.9.5, supports piping from stdin") public File INPUT; @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The output, downsampled, SAM or BAM file to write.")