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GenotypeGVCFs with same RG tags

grafalgrafal MPI TuebingenMember

Dear GATK forum,

Could you please clarify GenotypeGVCFs behaviour when some gvcfs share the same RG tag?

  • in scenario 1 (vertical): we have split single sample into 5 chromosomes using HaplotypeCaller -L option. Would GenotypeGVCFs merge 5 gvcf's correctly or should I merge them beforehand?
  • in scenario 2 (horizontal): we have same biological individual sequenced twice in two different runs. The two bam files were HaplotypeCalled separately and then GenotypeGVCFs'd together. Are the results inferior to HaplotypeCalling them together and then GenotypeGVCFs'ing (as suggested in thread below)?
  • if so, is the tool that @Geraldine_VdAuwera for recalculating made public in recent GATK versions?


Many many thanks! :)


Best Answer


  • EADGEADG KielMember ✭✭✭

    Hi @grafal,

    The first scenario, yes GenotypeGVCFS will merge them correctly. In WDL best practice pipeline, this way used for scatter & gather to save up computation time.

    The second scenario I don't know I this tool is ever made public or if its a function of CombineGVCFs now, but I think @Geraldine_VdAuwera and the other will know more. To be safe I would merge the bam files, as you already mentioned.

    Greetings from Kiel ;)


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