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.
understanding ValidateVariants output
I am trying to understand what does the number of records mean in ValidateVariants output? Notice in the below output for the VCF file it says checked 3814206 records when using GVCF it says 1 record. Using GATK version v3.7-0-gcfedb67 . thanks!
Output when i run ValidateVariants on a VCF (multi-sample)
Successfully validated the input file. Checked 3814206 records with no failures.
Done. There were 1 WARN messages, the first 1 are repeated below.
WARN 17:01:10,487 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
Output when running on a GVCF (multi-sample) file.
Successfully validated the input file. Checked 1 records with no failures. There were 2 WARN messages, the first 2 are repeated below. WARN 22:00:24,094 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation WARN 22:00:24,159 ValidateVariants - GVCF format is currently incompatible with allele validation. Not validating Alleles.