Changelog

CHANGELOG.md

@@ -36,6 +36,9 @@
 
 * `rsem/rsem_prepare_reference`: Prepare transcript references for RSEM (PR #89).
 
+* `bcftools`:
+  - `bcftools_norm`: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows (PR #144).
+
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1` (PR #72).

src/bcftools/bcftools_norm/config.vsh.yaml

@@ -34,7 +34,7 @@ argument_groups:
         alternatives: -o
         direction: output
         type: file
-        description: Output annotated file.
+        description: Output normalized VCF/BCF file.
         required: true
 
   - name: Options
@@ -68,7 +68,7 @@ argument_groups:
       - name: --fasta_ref
         alternatives: -f
         type: file
-        description: Reference sequence file.
+        description: Reference fasta sequence file.
 
       - name: --force
         type: boolean_true
@@ -160,7 +160,6 @@ argument_groups:
         description: | 
           Use multithreading with the specified number of worker threads.
 
-
 resources:
   - type: bash_script
     path: script.sh