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How can I create a GVCF from a FASTA file?
I have used the variant calling workflow and am interested in including a few outgroup samples (FASTA). What is the best way to generate gVCF files which indicate variants from my outgroups (FASTA) with respect to my reference genome (FASTA) so that I can then use the GenotypeGVCF tool to jointly genotype my samples and create a final VCF including variants called from my samples as well as my outroups?
Thank you for your help!