Dragen-gatk pipeline information ?
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12 days ago
quentin54520 ▴ 20

Hello all,

Has anyone ever tested the dragen-gatk version for the human germline genome? If so, have you obtained satisfactory results compared to classic gatk? What steps did you take?

germline gatk dragen wgs • 180 views
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Yes, yes, all recommended!

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More precisely ? For the moment there is no official pipeline and i don't found any clue toi begin in term of option and tools to run. I run : Fastp Bwa mem2 MarkduplicatesSpark CalibrateDragstrModel Haplotypecaller (dragen mode)

But then ?

Hard filter instead of vqsr ? With wich parameter ? I would like to have some first ideas so as not to start from nothing

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We run one sample on both DRAGEN and standard clinical pipeline and compared precision/recall/etc with different parameters.

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