deletion impact

Question

[HarperReed]

Hello, sorry for this wird question maybe :/ I am working on a specific gene and trying to detect known variants (for which I already know the positions and type of mutations). I run my detection algorithm, minipileup on my bam files, and then normalize the resulting VCF with the following commands:

bcftools norm -m- -o "$intermediate_vcf" "$input_path"
bcftools norm -f "$ref_genome" -cw -o "$final_vcf" "$intermediate_vcf"

Question: If there is a double deletion at positions N and N+1, could that affect other downstream variants I want to quantify? Or, since minipileup always references the original genome (ensuring positions stay aligned with the reference) and I have properly normalized my VCF, am I safe? I notice that in the VCF file, the REF column correctly shows the nucleotides from the reference sequence in their proper order.