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split multiallelic variants before VQSR and CNNScoreVariants, gatk team opinion

manolismanolis Member ✭✭✭
edited February 2019 in Ask the GATK team


if I remember well I saw in the forum a user to suggest to split the multiallelic variants before VQSR. I think that is something logical (I never done before), but I would like to know the opinion of the GATK team considering that the splitted-multiallelic variants (together with the other variants), at least in my case, should be used as input in the VQSR and the CNN steps.

Is it also good practice to LeftAlignAndTrimVariants before VQSR and CNN?

Many thanks

Post edited by manolis on


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