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.
Construct genome with gvcf or vcf file?
I have 100 rice accessions and their mapping files from DNA sequencing. My goal is to construct the genome for a specific region for each rice accession. Could I just use the gvcf file after initial varaint calling? If so, how could I guarantee the quality for those SNP/InDel sites? Or must I use the vcf file after final genotype call?