To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Recommendations on using different versions of GATK for variant calling and joint genotyping

jsreddy82jsreddy82 Mayo Clinic, Jacksonville, FL.Member

Dear GATK Team,

From what I understand, best practices recommend using the same version of GATK for variant calling (with HaplotypeCaller) and joint genotyping (with GenotypeGVCFs). Let's say, we found that GATK v3.4 has a better way of calling/reporting mutli-allelic variant calls. Will it be OK to have used HaplotypeCaller from v3.3 to call variants and then use GenotypeGVCFs from v3.4 to perform joint genotyping?

Thank You.
Joseph.

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    In general, yes, but we determined that certain combinations are ok, meaning we ran all the necessary validations in order to be able to use some GATK4 tools in our production pipeline. Specifically, we now do the pre-processing (BQSR) with GATK4, then generate GVCFs with HaplotypeCaller from 3.x (production is still on 3.7 iirc but 3.8 is fine too) and finally GenotypeGVCFs and related GenomicsDB tools from GATK4.

    So what you propose to do is ok. However what the OP proposes (mixing older versions), we have not validated and can therefore not guarantee results. There were more important changes between some of those versions, when the tools were still being hammered out -- as opposed to the move from 3.7/8 to GATK4 which is mostly just a port to the new framework, with few if any changes to the underlying algorithms.

Answers

  • Hi there,
    I wonder about the same. Is it fine to obtain gVCF files with the HaplotypeCaller -ERC GVCF mode from GATK 3.8 and then conduct joint genotyping of the gVCF files with GATK 4?

    Thanks

  • jsreddy82jsreddy82 Mayo Clinic, Jacksonville, FL.Member

    Don't know if this applicable to both our situations, but this issue was addressed here

  • jsreddy82jsreddy82 Mayo Clinic, Jacksonville, FL.Member

    @Sheila or @Geraldine_VdAuwera can you please confirm if this is still applicable to more recent versions of GATK?

    Thank you.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    In general, yes, but we determined that certain combinations are ok, meaning we ran all the necessary validations in order to be able to use some GATK4 tools in our production pipeline. Specifically, we now do the pre-processing (BQSR) with GATK4, then generate GVCFs with HaplotypeCaller from 3.x (production is still on 3.7 iirc but 3.8 is fine too) and finally GenotypeGVCFs and related GenomicsDB tools from GATK4.

    So what you propose to do is ok. However what the OP proposes (mixing older versions), we have not validated and can therefore not guarantee results. There were more important changes between some of those versions, when the tools were still being hammered out -- as opposed to the move from 3.7/8 to GATK4 which is mostly just a port to the new framework, with few if any changes to the underlying algorithms.

  • Thanks for the confirmation :)

  • jsreddy82jsreddy82 Mayo Clinic, Jacksonville, FL.Member

    @Geraldine_VdAuwera thank you for the clarification. Appreciate your response.

Sign In or Register to comment.