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.
FastaAlternateReferenceMaker for polyploid
Are there any tools similar to FastaAlternateReferenceMaker that can create fasta sequences from a pooled-sequencing vcf file? The sample data came from 25 pooled diploid individuals, so I created the vcf for ploidy = 50. I know that a similar question was asked concerning multiple-sample vcfs (https://gatkforums.broadinstitute.org/gatk/discussion/1654/fastaalternatereferencemaker-for-several-individuals), but this case is different since the samples were all pooled without barcodes.
Any suggestions would be appreciated. Thanks!