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Why using recommended pipeline with the HaplotypeCaller is better than UnifiedGenotyper?

HaoWangHaoWang ShanghaiMember

I have found some recommendation in the forum,your GATK team says it's better to use pipeline with the HaplotypeCaller .Why?Besides,why HaplotypeCaller has no -glm SNP or -glm INDEL options?
plz tell me,thank you!

Best Answer


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