From 939babc820cc5174a1d97a8b6bdb992ca6cedc09 Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 15 Sep 2011 21:05:51 -0400 Subject: [PATCH] Updating formating for ValidationAmplicons GATK docs --- .../sting/gatk/walkers/validation/ValidationAmplicons.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 01e8cd321..48cba6a1a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -61,7 +61,7 @@ import java.util.List; * CACGTTCGGcttgtgcagagcctcaaggtcatccagaggtgatAGTTTAGGGCCCTCTCAAGTCTTTCCNGTGCGCATGG[GT/AC*]CAGCCCTGGGCACCTGTNNNNNNNNNNNNNTGCTCATGGCCTTCTAGATTCCCAGGAAATGTCAGAGCTTTTCAAAGCCC * * are amplicon sequences resulting from running the tool. The flags (preceding the sequence itself) can be: - * + *
  * Valid                     // amplicon is valid
  * SITE_IS_FILTERED=1        // validation site is not marked 'PASS' or '.' in its filter field ("you are trying to validate a filtered variant")
  * VARIANT_TOO_NEAR_PROBE=1  // there is a variant too near to the variant to be validated, potentially shifting the mass-spec peak
@@ -72,10 +72,10 @@ import java.util.List;
  * END_TOO_CLOSE,            // variant is too close to the end of the amplicon region to give sequenom a good chance to find a suitable primer
  * NO_VARIANTS_FOUND,        // no variants found within the amplicon region
  * INDEL_OVERLAPS_VALIDATION_SITE, // an insertion or deletion interferes directly with the site to be validated (i.e. insertion directly preceding or postceding, or a deletion that spans the site itself)
- * 

+ *

* *

Examples

- * 

+ * 
  *    java
  *      -jar GenomeAnalysisTK.jar
  *      -T ValidationAmplicons