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How can I create a GVCF from a FASTA file?

KatieKatie United StatesMember ✭✭

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!

Issue · Github
by Sheila

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Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Katie, unfortunately there's no good way to do that directly with GATK. Our tools are designed to process high throughput sequencing data, where you have many short sequences adding up evidence for variation. A Fasta doesn't have the quality information we rely on to make these calls. I expect that other software packages exist that would be more appropriate to your use case.

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