Undoing large genomic deletions using minimap and bcftools

Question

[Jamie]

I'm trying to undo large genomic deletions in the genome of an organism.

I have a draft genome assembly of the organism using cryopreserved samples from before the regions were deleted and a newly assembled reference genome lacking these regions of interest.

I am using minimap2 to perform a draft assembly to ref. genome alignment and then to use BCFtools to generate genotype likelihoods, call variants, and to create consensus sequences (code below). My question is - am I thinking about this correctly? Are there better ways of doing this and does any of this make sense?

Code:

minimap2 -ax asm20 ${ref_genome} ${assembly} | samtools sort -o alignment.bam
bcftools mpileup -Ou -f ${ref_genome} alignment.bam | bcftools call --ploidy 1 -mv -M -Oz -o test.vcf.gz
bcftools index test.vcf.gz
bcftools consensus -H LA -f ${ref_genome} test.vcf.gz > consensus.fa