To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Single-Sample Genotyping: Different Workflow?

james_lawlorjames_lawlor Huntsville, ALMember

If I need to independently call and genotype a single sample, is there a different workflow or set of GATK tools and settings that I ought to use instead of using haplotypecaller to generate a GVCF and then using genotypegvcfs to genotype a "batch of 1"?

(In other words, is there another tool or setting that will go directly from BAM to VCF and give better or significantly different results than above.)

I'm aware of the many benefits of the GATK best practices workflow for singly-calling BAMs to GVCFs and then jointly genotyping the batches; however, at the moment I am doing some benchmarking for a project where a joint-calling pipeline may not be feasible and we may need to call each sample independently.


Best Answer


Sign In or Register to comment.