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Single-Sample Genotyping: Different Workflow?

james_lawlorjames_lawlor Huntsville, ALMember

Hi,
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.

Thanks!
James

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