Entering edit mode
2.6 years ago
quentin54520
▴
120
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?
Yes, yes, all recommended!
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
We run one sample on both DRAGEN and standard clinical pipeline and compared precision/recall/etc with different parameters.