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FastaAlternateReferenceMaker for several individuals ?
Hi GATK team,
I have a VCF file (from GATK) containing variants for a total of 20 individuals and I'm wondering how to get the consensus sequences for each individual regarding its own polymorphism. Some individuals may not show polymorphism at a particular position in a contig whereas some others may. I've checked the GATK dedicated tool (FastaAlternateReferenceMaker) but it doesn't answer my question as only one consensus is generated. My requirement would be to get as many outputs files (containing consensus file) as mapped individuals.
Is there anyway to get this task achieved using GATK?