Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

(How to) Call common and rare germline copy number variants Follow


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    Enrico Cocchi

    Is there any way to get the log2 output instead of the CN from PostprocessGermlineCNVCalls?

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    Calvin Hung

    Hi, I believe the *.tsv files in the tutorial_11684.tar.gz either from the GoogleDrive or from the FTP site are deprecated and cannot run through GermlineCNVCaller since GATK v4.1.x.x. I managed to hack the format and fixed it myself. You might want to update the tutorial files as well.

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    Ruqian Lyu


    Thanks for the great tutorial.

    I'm trying to run the pipeline for 300 low coverage samples (~5X). At the step of running GermlineCNVCaller, I'm seeing the tool keeps increasing the number of epochs because CNV calling is not converged. It is now at 50 epochs. Is this something expected or is it possible the optimisation procedure has been "trapped"  ?

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