I have a bam file and corresponding vcf file from some source. I am trying to slice the DNA across its mutation location to feed into one of the algorithms.
I wanted to know what is the right way to do this. I have two options
- I can create a genome assembly/contigs from the bam file and then slice it using mutation information from vcf file.
- I can take a reference genome and then slice it from vcf file.
What are the pros and cons of either method?