I'm asking here before I go off half-cocked and try to build my own solution.
Simply put, I have been using the reference GRCh38, created BAM files via
HiSAT2, and then BCF files using
samtools mpileup | bcftools call | bcftools norm.
The BCF tools include the REF/REF matches, and the BCF file is for a single diploid organism (one human sample) ... so the BCF file contains only
The next step is I want to create a new reference file (I assume .fastq is best) and incorporate the BCF file results into that reference.
Is there a tool/process already in place for something like this?