diff --git a/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java b/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java index 78c32ed02..9823e524a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java +++ b/public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java @@ -46,6 +46,7 @@ public class DeprecatedToolChecks { deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)"); deprecatedGATKWalkers.put("AlignmentWalker", "2.2 (no replacement)"); deprecatedGATKWalkers.put("CountBestAlignments", "2.2 (no replacement)"); + deprecatedGATKWalkers.put("SomaticIndelDetector", "2.0 (replaced by the standalone tool Indelocator; see Cancer Tools documentation)"); } // Mapping from walker name to major version number where the walker first disappeared and optional replacement options