Hi GATK Users,

Happy Thanksgiving!
Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!

GATK Staff

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.