Change Sniffles regenotyping pipeline

Individually regenotyping of the imported VCF files with Sniffles. The two resulting VCFs are then merged together.

scripts/Spike/2b_SV.sh

@@ -8,13 +8,17 @@
 
 READ_LENGTH=$1
 VAF=$2
-MERGED_VCF=$3
-MOD_BAM=$4
-OUTPUT_VCF=$5
-REFERENCE=$6
-OUTPUT_PFX=$7
+VCF_A=$3
+VCF_B=$4
+MOD_BAM=$5
+OUTPUT_VCF=$6
+REFERENCE=$7
+OUTPUT_PFX=$8
+
+echo "VCF_A: $VCF_A"
+echo "VCF_B: $VCF_B"
+echo "MOD_BAM: $MOD_BAM"
 
-# Descide which READ_LENGTH was selected
 if [ "$READ_LENGTH" = "short" ]; then
 
     # https://github.com/Illumina/paragraph
@@ -24,7 +28,12 @@ if [ "$READ_LENGTH" = "short" ]; then
 
 elif [ "$READ_LENGTH" = "long" ]; then
     echo "Input is 'long' starting Sniffles2"
-    sniffles --input $MOD_BAM --genotype-vcf $MERGED_VCF --sample-id mosaicSim --vcf $OUTPUT_VCF
+    sniffles --input $MOD_BAM --genotype-vcf $VCF_A --sample-id mosaicSim --vcf "${OUTPUT_VCF}.vcf1.vcf"
+    sniffles --input $MOD_BAM --genotype-vcf $VCF_B --sample-id mosaicSim --vcf "${OUTPUT_VCF}.vcf2.vcf"
+
+    # Merge the two VCF files with bcftools
+    bcftools merge --force-samples -O z --write-index -o $OUTPUT_VCF $VCF_A $VCF_B
+
 else
     echo "Error: Invalid input"
 fi