extract fast from bam taking SV into account

[EHC]

Hi,
I have a bam file that includes a big indel and a translocation. I wish to extract a new reference fasta file with the SV (without the deleted region and with the translocation). I also preform a de novo assembly so I want to compare the two outputs I got. What is the wright way to do so?


I tried:

samtools mpileup -uf ref.fa test.bam | bcftools call -c | vcfutils.pl vcf2fq > test.fastq

I do not think it includes the SVs inside. Any suggestions?

Thanks