adding scripts for mitomap annotation and VCf plots

mitnanex_reference.sh

@@ -248,8 +248,11 @@ pipe_exec(){
             #map_reads
             #variant_calling
             #haplogroup_class
+            #mitomap
             #annotate_vcf
-            annotate_mito
+            #plot_vcf
+            #annotate_mito
+
 
 
         else

scripts/mitomap.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+mitomap() {
+    ## Connect to MITOMAP API to annotate variants, haplogroup, clinic relevance
+    custom_prints "Annotate variants with Mitomap" }
+
+    mitomap_out="$WD/variant_annot.mitomap.txt"
+
+    $exec_path/scripts/mitomap.py $vcf_file $mitomap_out
+
+    echo "$timestamp [ATTENTION]: Variant annotations are at" $mitomap_out
+
+}

scripts/plot_vcf.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+plot_vcf(){
+    ## PLOT VCF STATS
+
+    custom_prints "Plot VCF statistics"
+
+    vcfplotsdir="$WD/vcf_plots"
+    create_wd $vcfplotsdir
+
+
+    vcfstats --vcf $$vcf_file --outdir $vcfplotsdir \
+    --config "$exec_path/scripts/plots_vcf.toml" \
+    --macro "$exec_path/scripts/custom_macro.py"
+
+    echo "$timestamp [ATTENTION]: VCF plots are at" $vcfplotsdir
+
+}