The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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!