modified minimap2 option on liftoff to handle small rnas

juanjo255 · Jan 24, 2025 · f20b5b8 · f20b5b8
1 parent e8e0aed
commit f20b5b8
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/mitnanex_reference.sh b/mitnanex_reference.sh
@@ -281,9 +281,9 @@ pipe_exec(){
             fi
             vars_definition
             map_reads
-            #variant_calling
+            variant_calling
             #annotate_vcf
-            #plot_vcf
+            plot_vcf
             #annotate_mito
             #mitomap
 

diff --git a/scripts/annotate_mito.sh b/scripts/annotate_mito.sh
@@ -8,9 +8,9 @@ annotate_mito(){
     create_wd $annot_folder
     annot_file="$annot_folder/$prefix.liftoff.gff"
 
-    liftoff -g $ref_gff "$consensus_mitogenome" \
+    liftoff -g $ref_gff "$consensus_mitogenome" -mm2_options="-a --end-bonus 0 --eqx -N 5 -p 0.8 -k10 -w3" \
     "$exec_path/refseqMT/chrMT.fna" -o $annot_file
 
     echo "$timestamp [ATTENTION]: Mitochondrial consensus annotation file is at" $annot_file
 
-}
+}
diff --git a/scripts/plots_vcf.toml b/scripts/plots_vcf.toml
@@ -1,7 +1,7 @@
 ## PARAMETERS FOR PLOTTING VCF
 
 # General options
-devpars = {width = 1000, height = 1000, res = 200}
+devpars = {width = 1300, height = 1000, res = 200}
 passed = true
 
 # Plots