From c193f52e5de69e8dd837f42aae299a31ed5b016e Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Wed, 17 Aug 2011 16:29:45 -0400
Subject: [PATCH] Fixed up examples: pasting from wiki still had old rod syntax

---
 .../gatk/walkers/beagle/BeagleOutputToVCFWalker.java   | 10 +++++-----
 .../gatk/walkers/beagle/ProduceBeagleInputWalker.java  |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
index aca176bc2..51fe543df 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
@@ -64,11 +64,11 @@ import static java.lang.Math.log10;
  * <pre>
  *     java -Xmx4000m -jar dist/GenomeAnalysisTK.jar \
  *      -R reffile.fasta -T BeagleOutputToVCF \
- *      -B:variant,VCF input_vcf.vcf \
- *      -B:beagleR2,BEAGLE /myrun.beagle_output.r2 \
- *      -B:beaglePhased,BEAGLE /myrun.beagle_output.phased \
- *      -B:beagleProbs,BEAGLE /myrun.beagle_output.gprobs \
- *      --out output_vcf.vcf
+ *      -V input_vcf.vcf \
+ *      -beagleR2:BEAGLE /myrun.beagle_output.r2 \
+ *      -beaglePhased:BEAGLE /myrun.beagle_output.phased \
+ *      -beagleProbs:BEAGLE /myrun.beagle_output.gprobs \
+ *      -o output_vcf.vcf
  *      </pre>
 
  <p> Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them </p>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
index 6ac817555..07793fd7b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
@@ -68,7 +68,7 @@ import java.util.*;
  * <pre>
  *     java -Xmx2g -jar dist/GenomeAnalysisTK.jar -L 20 \
  *      -R reffile.fasta -T ProduceBeagleInput \
- *      -B:variant,VCF path_to_input_vcf/inputvcf.vcf -o path_to_beagle_output/beagle_output
+ *      -V path_to_input_vcf/inputvcf.vcf -o path_to_beagle_output/beagle_output
  * </pre>
  *
  */