Stranger

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+1. Added `Stranger` annotation of `ExpansionHunter` output in the repeat expansion workflow.
+
 ### `Changes`
 
 1. Changed from `delly_call` to `delly_sr`. Delly v2.6.0

conf/modules.config

@@ -284,6 +284,10 @@ process {
         ext.tabix = true
     }
 
+    withName: "^.*BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:STRANGER\$" {
+        ext.prefix = { "${meta.id}.stranger" }
+    }
+
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         CONCAT OUTPUTS

docs/CITATIONS.md

@@ -63,6 +63,8 @@
 
 - [smoove](https://github.com/brentp/smoove)
 
+- [Stranger](https://github.com/Clinical-Genomics/stranger)
+
 - [svync](https://github.com/nvnieuwk/svync)
 
 - [Tabix](https://academic.oup.com/bioinformatics/article/27/5/718/262743)

docs/output.md

@@ -141,7 +141,7 @@ RRE calling runs all selected callers individually and merges the calls after. O
 
 </details>
 
-There are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Such repeat regions can expand to a size much larger than the read length and thereby cause a disease. Fragile X Syndrome, ALS, and Huntington's Disease are well known examples. [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat.
+There are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Such repeat regions can expand to a size much larger than the read length and thereby cause a disease. Fragile X Syndrome, ALS, and Huntington's Disease are well known examples. [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat. ExpansionHunter's output is then annotated with [Stranger](https://github.com/Clinical-Genomics/stranger), which attaches pathogenicity classification (`STR_STATUS`, normal/pathologic thresholds) from the variant catalog.
 
 ### SV annotation
 

modules.json

@@ -117,6 +117,11 @@
                         "git_sha": "fdcc3976e728b5d6ffc3f15979905829531e6072",
                         "installed_by": ["modules"]
                     },
+                    "stranger": {
+                        "branch": "master",
+                        "git_sha": "90e0aedba7e6b6cd6a0a7edc612c3f54f0caa663",
+                        "installed_by": ["modules"]
+                    },
                     "strvctvre/strvctvre": {
                         "branch": "master",
                         "git_sha": "fdcc3976e728b5d6ffc3f15979905829531e6072",