Updating naming convention

Changed naming von VCF_1 to VCF_A and VCF_2 to VCF_B

scripts/Spike/2b_re-genotyping_main.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Input variables are: VARIANT, VAF, VCF_1, VCF_2, MOD_BAM, OUTPUT_DIR, READ_LENGTH
+# Input variables are: VARIANT, VAF, VCF_A, VCF_B, MOD_BAM, OUTPUT_DIR, READ_LENGTH
 # VARIANT can be either SNV or SV
 # READ_LENGTH can be either SHORT or LONG for SVs
 
@@ -14,8 +14,8 @@
 
 VARIANT=$1
 VAF=$2
-VCF_1=$3
-VCF_2=$4
+VCF_A=$3
+VCF_B=$4
 MOD_BAM=$5
 OUTPUT_DIR=$6
 READ_LENGTH=$7
@@ -24,15 +24,17 @@ OUTPUT_VCF="${OUTPUT_DIR}/output_genotypes.vcf"
 OUTPUT_VCF_FILTERED="${OUTPUT_DIR}/output_genotypes_filtered.vcf"
 REFERENCE=${8}
 
+mkdir -p $OUTPUT_DIR
+
 # Merge the two VCF files with bcf tools
-bcftools merge --force-samples -O z --write-index -o $MERGED_VCF $VCF_1 $VCF_2
+bcftools merge --force-samples -O z --write-index -o $MERGED_VCF $VCF_A $VCF_B
 
 if [ "$VARIANT" = "SNV" ]; then
     echo "Input is 'SNV'"
     ./2b_SNV.sh $READ_LENGTH $VAF $MERGED_VCF $MOD_BAM $OUTPUT_VCF $REFERENCE
 elif [ "$VARIANT" = "SV" ]; then
     echo "Input is 'SV'"
-    ./2b_SV.sh $READ_LENGTH $VAF $MERGED_VCF $MOD_BAM $OUTPUT_VCF $REFERENCE "Spike_out"
+    ./2b_SV2.sh $READ_LENGTH $VAF $VCF_A $VCF_B $OUTPUT_VCF "${OUTPUT_DIR}/output_genotypes" $REFERENCE "Spike_out"
 else
     echo "Error: Invalid input"
 fi