The frontline support team will be offline as we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and available to answer questions on the forum on March 25th 2019.

HaplotypeCaller in Gatk4 vs Gatk3.5

Dear colleagues, I noticed that latest "5 dollar pipeline" uses HaplotypeCaller from gatk3.5 not gatk4.
Could you comment is it OK now to use HaplotypeCaller from gatk4 - if no, what are potential problems with using it?


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    The pipeline uses 3.5 because at the time of building, GATK4 was not yet validated/ready to use. Now that GATK4 is validated, there should be no issue using it in the pipeline :smile: The team has just not made the switch yet.


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