From 96344c6b62df84d4727bbbd8307d03f88da0f0c1 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 31 Oct 2012 12:35:45 -0400 Subject: [PATCH] Add note to realigner docs --- .../sting/gatk/walkers/indels/IndelRealigner.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 998894fbf..8f2528e23 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -236,6 +236,8 @@ public class IndelRealigner extends ReadWalker { * then extensions (".bam" or ".sam") will be stripped from the input file names and the provided string value will be pasted on instead; 2) if the * value ends with a '.map' (e.g. input_output.map), then the two-column tab-separated file with the specified name must exist and list unique output * file name (2nd column) for each input file name (1st column). + * + * Note that some GATK arguments do NOT work in conjunction with nWayOut (e.g. --disable_bam_indexing). */ @Argument(fullName="nWayOut", shortName="nWayOut", required=false, doc="Generate one output file for each input (-I) bam file") protected String N_WAY_OUT = null;