How do you customize a reference genome, say, hg19, and make into a personalized reference genome in fasta format? I don't have the phased sequence information, but I have the fastq's, bam, and vcf formats.
Sounds like a job for GATK FastaAlternateReferenceMaker
Perfect, just what I need. Thanks!
Glad to help. If my answer resolved your question you should accept it to mark this question as solved.