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Recommended/required sequencing depth for standard diploid, whole-genome, germline variant calling
I was searching the GATK best practices for a recommended or required sequencing depth for standard whole-genome germline variant calling on a diploid species (humans, specifically). I know general word of mouth is at least 30x, but can you clarify GATK's recommendations or requirements?
1. I know this is not super easy to determine, but what is the approximate required depth for UnifiedGenotyped (GATK v3.X)? How about recommended?
2. Similarly, what are the required and recommended depths for HaplotypeCaller?
I'm trying to determine the approximate coverage at which you would not trust a specific variant. I realize this is very context specific, but a general recommendation would be super helpful.