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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.