Add samples to CNV analysis without re-running all samples?

Follow

Joel Wallenius

• November 25, 2024 14:20

Hello!

I'm wondering if I can add one or two samples to my CNV-calling analysis without having to re-run all 100+ samples (human WGS) from scratch. How would I do that? It takes a month to run all samples, so I'd rather not re-run every time we add only a few samples to our cohort.

Big thanks in advance <3

/Joel

 

a) GATK version used:

The Genome Analysis Toolkit (GATK) v4.2.6.1
HTSJDK Version: 2.24.1
Picard Version: 2.27.1

b) Exact command used:

gatk GermlineCNVCaller --run-mode COHORT et c.

c) Entire program log:

Not Applicable

0

• 

  Gökalp Çelik

  • November 25, 2024 16:17

  Hi Joel Wallenius

  Yes you can do it. Actually we have a case mode available for the GCNV workflow which uses a model created using the cohort mode and generates the same segmented CNV calls for your additional files. Since the model is created already case mode runs quite fast. 

  I hope this helps.

  Regards. 

  0

  Comment actions Permalink

Please sign in to leave a comment.