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 distinguish between Missing and ReF in gVCF
I have a naive query which might have discussed earlier. I tried to find in the forum but did not succeed.
Consider gVCF files produced for 3 different samples (single-sample variant calling) and genotyping gVCF to VCF generates the list of only variant sites. When it is required to find the shared variants between 3 samples, if one of the sample has no variant at that particular site in the VCF file, how could it be interpreted, Is it missing due to lack of reads or REF?