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.
How to generate a database SNP with non-model species?
Foer generating a vcf file contain multiple samples, It seems that I need a database SNP or variants
I want to generate vcf file containing multiple samples of birds for analyzing population genomic data with plink,
so I think I can use UnifiedGenotyper to generate the vcf.
From the tooldocs of UG, I know that I may need a database.vcf files to let GATK know how many substitution site in birds genome, but there's no known site of SNPs or INDELs of my research system before.
I already have 40 birds' variants which have been done recalibration two times.
So, can I generate the know site from my samples' vcf files for calling variants containing multiple samples ?