Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Is there any way to take vcf data and output 2 fastas - one of each of the sample's alleles?
So I looked at using the ReadBackedPhasing tool or the Haplotype caller but I already have a calling pipeline setup that works well with my data and I'm really just looking at a way to leverage the vcfs I generate to make consensus fastas of each allele. Sample data is diploid, currently I export to a fasta with ambiguity codes and use dnasp to generate the allele fastas, but I know there's got to be a good way to leverage that vcf information.