From 717cd4b912df8787deee2f9e6ec61d26bf05ea98 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 7 Feb 2012 13:30:54 -0500 Subject: [PATCH] Document -L unmapped --- .../sting/gatk/arguments/GATKArgumentCollection.java | 1 + 1 file changed, 1 insertion(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index b3a1e2488..8ec707801 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -75,6 +75,7 @@ public class GATKArgumentCollection { * Using this option one can instruct the GATK engine to traverse over only part of the genome. This argument can be specified multiple times. * One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals). * Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf). + * To specify the completely unmapped reads in the BAM file (i.e. those without a reference contig) use -L unmapped. */ @Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false) public List> intervals = null;