I would like to modify a reference genome fasta file using a list of position in bed file format. The bed file contains positions like this:
chr1 17716 C G chr1 17925 A G chr1 18115 C T
So for example I would like to change the position at chr1 17716 from C to G in the fasta file. I have seen some python packages and a GATK tool for modifying a fasta file using a list of VCF positions but was wondering if there was any tool that would do this using a bed file as input rather than a VCF. Or would it be better to convert the bed file to VCF format by adding a VCF header (I'm not sure if this would work?).
Thanks in advance for your help.