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.
gvcf or final vcf used to construct accession specific genome
I have 100 rice accessions and its DNA sequencing bam files. My goal is to construct the genome in a specific region for each rice accession. Could I directly use the gvcf file from the variant call? Or it is better to use the vcf file after final genotype call? If I use gvcf file, is there any filtering step I should use to guarantee the quality? Thanks.