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Returning different files for each haplotype using FastaAlternateReferenceMaker
I'm trying to generate FASTA files from a VCF file. My VCF files contain haplotype information (as '0|1', '0|0', and '1|0').
I want different FASTA files for each haplotype, but can only get one using the FastaAlternateReferenceMaker utility.
Is there a way to get two different FASTA files?
Thanks in advance!