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vcf / GVCF result sets differ

It seems that running HaplotypeCaller with -ERC GVCF and then running GenotypeGVCFs -stand_call_conf 30 -stand_emit_conf 30 gives a different vcf than HaplotypeCaller -stand_call_conf 30 -stand_emit_conf 30 (on a single sample). Is that expected? I tried versions 3.2 and 3.5.

Tag along question: I've tried to be a good citizen and post questions on existing topics in this forum (instead of starting yet a duplicate thread) but these never get answered. Is it always better to post a new question?

Thanks for your help.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    We aim to answer everything regardless of where it gets posted. You may have been unlucky and posted hard questions at especially busy times... I'll be going through our backlog over the weekend and will try to catch up on any unanswered questions.

    For this one, in a nutshell, minor differences are expected, but nothing major. Did you quantify the differences you observed?

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