I have some software which takes fastas as the input. I need to include SNVs and InDels from a VCF into the reference hg38 and then use this.
The problem is, I don't know of an algorithmically sound way to do this.
Are there any existing software packages which could do this efficiently? Is it easier to output a FASTA, or a bam (and then convert to a FASTA)?
What about if I wanted to do the same with a bedpe of germline structural variants?