Closed:Making reference fasta file from aligned sam file or bed file

Question

[vkgaur25]

I have cancer panel data targeting 212 amplicons. I want to use a reference genome that only contains sequences from these 212 amolicons for mapping instead of whole human genome. I think I can create a bed file from amplicon coordinates and fetch sequences. Is that right approach becuase many amplicons have different locations on same chromosome and repeated (or duplicated)chromosome numbers in bed files create a problem in indexing and sorting (which has been the case when I tried to do this). Can I also have my new reference from the mapped files (sam or bam which are obtained after aligning to whole genome) only for these 212 regions?

I hope it’s not confusing; Kindly help with suggestions.

thanks in advance.