Joint calling on individual gvcfs vs merged gvfs

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gen1234

• February 19, 2020 18:24
• Edited

Can you please provide
a) GATK version used

3.4

b) Exact GATK commands used

N/A

c) The entire error log if applicable.

N/A

I am trying to do joint calling on multiple samples from this workflow:

 

https://gatk.broadinstitute.org/hc/en-us/articles/360035890411-Calling-variants-on-cohorts-of-samples-using-the-HaplotypeCaller-in-GVCF-mode

 

This document reads like you need to aggregate individual gvcfs to one file to run GenotypeGVCF. This takes a very long time with hundreds of samples, even when splitting by chromosome.

 

This post actually seems counter and suggests you can run GenotypeGVCF on multiple individual samples:

https://gatkforums.broadinstitute.org/gatk/discussion/3973/combinegvcfs-performance

 

If I run GenotypeGVCF on unmerged GVCF (one for each sample) do I still get the benefits of "joint calling"? 

0

• 

  Bhanu Gandham

  • February 19, 2020 18:47

  Hi gen1234

   

  We do not support GATK3 anymore. Please upgrade to the latest GATK4.1.4.0 version.

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