Update SOP_alignment_variant_annotation.md

docs/SOP_alignment_variant_annotation.md

@@ -255,7 +255,7 @@ sbatch --export=PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=$SCRIPTS/trio_
 
 ```
 cd $OUTPUT_DIR/${short_project_id}_${version}
-rm families/*/*.bam*
+rm families/*/*/*.bam*
 ```
 
 12. Clean up. Clear the work and logs directories. Move the bcbio YAML configuration files into the results folder for the project. Retain reads for samples in families where one sample has failed QC, using a list `retain\_for\_rerun.txt`. These will likely be required for later runs, and it is simpler to regenerate config YAML files if it is not necessary to re-do symlinks/read merging.
@@ -267,6 +267,9 @@ rm -r *
 cd $LOGS_DIR
 rm -r *
 
+cd $PARAMS_DIR
+rm -r *
+
 mkdir -p $OUTPUT_DIR/${short_project_id}_${version}/config/
 mv $CONFIG_DIR/${short_project_id}_${version}*.yaml $OUTPUT_DIR/${short_project_id}_${version}/config/