I asked nicely and got nothing. Then I threatened and still got nothing. So I am carrying through on my threats. Guillermo, you have a short reprieve because you were away on vacation, but let's get yours done tomorrow afternoon.

public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java

@@ -60,6 +60,9 @@ import java.util.*;
  * and/or percentage of bases covered to or beyond a threshold.
  * Additionally, reads and bases can be filtered by mapping or base quality score.
  *
+ * <b>If any of the command-line arguments for this tool are not clear to you,
+ * please email chartl at broadinstitute dot org and he will gladly explain them in more detail.</b>
+ *
  * <h2>Input</h2>
  * <p>
  * One or more bam files (with proper headers) to be analyzed for coverage statistics

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java

@@ -77,6 +77,11 @@ import java.util.*;
  * if even a weak evidence for the same indel, not necessarily a confident call, exists in the first sample ("Normal"), or as somatic
  * if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
  * only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
+ *
+ * <b>If any of the general usage of this tool or any of the command-line arguments for this tool are not clear to you,
+ * please email asivache at broadinstitute dot org and he will gladly explain everything in more detail.</b>
+ *
+ *
  */
 @ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
 public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {

public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java

@@ -39,6 +39,9 @@ import java.util.List;
  * reasons why the site may fail validation (nearby variation, for example).
  * </p>
  *
+ * <b>If any of the command-line arguments for this tool are not clear to you,
+ * please email chartl at broadinstitute dot org and he will gladly explain them in more detail.</b>
+ *
  * <h2>Input</h2>
  * <p>
  * Requires a VCF containing alleles to design amplicons towards, a VCF of variants to mask out of the amplicons, and an