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Current status of GATK4 GermlineCNVCaller tools and best practices.

WimSWimS Member
edited February 1 in Ask the GATK team


I would like to try out GATK4 for discovering or genotyping germline CNV's in a cohort of few hundred whole genome sequenced samples. I work with non-human species data, but the genome sizes are almost the same as human or smaller.

The best practice documentation for germline CNV calling is still empty.

According the gatk4- JAR file germline CNV calling tools are already included.
java -jar ./gatk4-
USAGE: [-h]--------------------------------------------------------------------------------------
Copy Number Variant Discovery: Tools that analyze read coverage to detect copy number variants.
AnnotateIntervals (BETA Tool) Annotates intervals with GC content
CallCopyRatioSegments (BETA Tool) Calls copy-ratio segments as amplified, deleted, or copy-number neutral
CombineSegmentBreakpoints (EXPERIMENTAL Tool) Combine the breakpoints of two segment files and annotate the resulting intervals with chosen columns from each file.
CreateReadCountPanelOfNormals (BETA Tool) Creates a panel of normals for read-count denoising
DenoiseReadCounts (BETA Tool) Denoises read counts to produce denoised copy ratios
DetermineGermlineContigPloidy (BETA Tool) Determines the baseline contig ploidy for germline samples given counts data.
GermlineCNVCaller (BETA Tool) Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.
ModelSegments (BETA Tool) Models segmented copy ratios from denoised read counts and segmented minor-allele fractions from allelic counts
PlotDenoisedCopyRatios (BETA Tool) Creates plots of denoised copy ratios
PlotModeledSegments (BETA Tool) Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates

Can you give some more information about what the current status is of the GATK4 GermlineCNVCaller tools and if you have an estimation for when the best practices for these tools should be available?

It would also be nice if you can give an idea if the GATK4 GermlineCNVCallertools tools are expected to work for non-human species, e.g. other vertebrates, simple / complex plants genomes and bacteria.

Thank you.

Issue · Github
by Sheila

Issue Number
Last Updated

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I just asked the developer, and we will get back to you soon.


  • WimSWimS Member

    @Sheila Hi, is there any news on this subject?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Sorry, I just pinged the developer again. Hopefully, I will have a response for you by tomorrow or Wednesday. Please post again if you do not hear from me by the end of the week.


  • WimSWimS Member

    Hi, is there any update on when the GermlineCNVCaller pipeline docs should become available? Thank you .

  • LYaoLYao Member

    Hi, I am also wondering the status of GATK4 GermlineCNVCaller tools and best practices. https://software.broadinstitute.org/gatk/best-practices/workflow?id=11148 . Thank you

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @WimS @LYao

    I don't have an ETA for you, but the team is working on them.


  • LYaoLYao Member

    @Sheila Thank you! I wonder if there is a manual for GATK4 GermlineCNVCaller that I can follow? I am trying to call germline CNVs in a timely manner. It would be great if you could give me suggestions about CNV calling in terms of gatk or in general. Thanks!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I know the team is working on it/refining the workflow. But, I don't have a good estimate of when we will share it. Sorry. I will see if the team can give some basic outline as least


  • WimSWimS Member

    Hi @Sheila Is there any news on the best practice document will be available for Germline CNV calling?

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @WimS

    We are working on this. I can't give you a timeline yet sorry, but it will be uploaded here.


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